From 8f8d5672f317bb1df03f85b3f8edea32c59e5542 Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Tue, 21 Feb 2023 18:13:34 -0500 Subject: [PATCH] Fix an NPE in CRAMRecordReadFeatures.restoreReadBases (#1655) * Fix an NPE in CRAMRecordReadFeatures.restoreReadBases() when reading crams with embedded references. * Fix for https://github.com/igvteam/igv/issues/1286 --- .../structure/CRAMRecordReadFeatures.java | 3 + .../samtools/CRAMReferencelessTest.java | 32 +- .../htsjdk/samtools/cram/testIGV1286.cram | Bin 0 -> 33017 bytes .../samtools/cram/testIGV1286.cram.crai | Bin 0 -> 51 bytes .../htsjdk/samtools/cram/testIGV1286.sam | 1324 +++++++++++++++++ 5 files changed, 1357 insertions(+), 2 deletions(-) create mode 100644 src/test/resources/htsjdk/samtools/cram/testIGV1286.cram create mode 100644 src/test/resources/htsjdk/samtools/cram/testIGV1286.cram.crai create mode 100644 src/test/resources/htsjdk/samtools/cram/testIGV1286.sam diff --git a/src/main/java/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.java b/src/main/java/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.java index d6e5b205cf..1c081e6dc2 100644 --- a/src/main/java/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.java +++ b/src/main/java/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.java @@ -495,6 +495,9 @@ public static byte[] restoreReadBases( } private static byte getByteOrDefault(final byte[] array, final int pos, final byte outOfBoundsValue) { + if (array == null) { + return outOfBoundsValue; + } return pos >= array.length ? outOfBoundsValue : array[pos]; diff --git a/src/test/java/htsjdk/samtools/CRAMReferencelessTest.java b/src/test/java/htsjdk/samtools/CRAMReferencelessTest.java index eefbaf7d22..c8e580d2d8 100644 --- a/src/test/java/htsjdk/samtools/CRAMReferencelessTest.java +++ b/src/test/java/htsjdk/samtools/CRAMReferencelessTest.java @@ -14,7 +14,7 @@ public class CRAMReferencelessTest extends HtsjdkTest { private static final File TEST_DATA_DIR = new File("src/test/resources/htsjdk/samtools/cram"); @Test - private void testReadCRAMWithEmbeddedReference() throws IOException { + public void testReadCRAMWithEmbeddedReference() throws IOException { try (final SamReader cramReader = SamReaderFactory.makeDefault() .validationStringency(ValidationStringency.LENIENT) .referenceSource(new ReferenceSource(new File(TEST_DATA_DIR, "human_g1k_v37.20.21.1-100.fasta"))) @@ -24,16 +24,44 @@ private void testReadCRAMWithEmbeddedReference() throws IOException { .open(new File(TEST_DATA_DIR, "referenceEmbedded.NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram"))) { final Iterator cramIterator = cramReader.iterator(); final Iterator cramEmbeddedIterator = cramReaderEmbedded.iterator(); + int count = 0; while (cramIterator.hasNext() && cramEmbeddedIterator.hasNext()) { + count++; final SAMRecord cramRecord = cramIterator.next(); final SAMRecord cramRecordEmbedded = cramEmbeddedIterator.next(); Assert.assertEquals(cramRecordEmbedded, cramRecord); } + Assert.assertTrue( count >0, "Expected reads but there were none."); } } + // test for https://github.com/igvteam/igv/issues/1286 + // cram was generated subset from an example cram using samtools and -O no_ref @Test - private void testReadCRAMNoReferenceRequired() throws IOException { + public void testForNPE() throws IOException { + try (final SamReader cramReader = SamReaderFactory.makeDefault() + .validationStringency(ValidationStringency.LENIENT) + .open(new File(TEST_DATA_DIR, "testIGV1286.sam")); + final SamReader cramReaderEmbedded = SamReaderFactory.makeDefault() + .validationStringency(ValidationStringency.LENIENT) + .open(new File(TEST_DATA_DIR, "testIGV1286.cram"))) { + final Iterator cramIterator = cramReader.iterator(); + final Iterator cramEmbeddedIterator = cramReaderEmbedded.iterator(); + int count = 0; + while (cramIterator.hasNext() && cramEmbeddedIterator.hasNext()) { + count++; + final SAMRecord cramRecord = cramIterator.next(); + final SAMRecord cramRecordEmbedded = cramEmbeddedIterator.next(); + Assert.assertEquals(cramRecordEmbedded, cramRecord); + } + Assert.assertEquals(count, 2); + Assert.assertFalse(cramIterator.hasNext()); + Assert.assertFalse(cramEmbeddedIterator.hasNext()); + } + } + + @Test + public void testReadCRAMNoReferenceRequired() throws IOException { // test reading a cram with no reference compression (RR=false in compression header) try (final SamReader samReader = SamReaderFactory.makeDefault() .validationStringency(ValidationStringency.LENIENT) diff --git a/src/test/resources/htsjdk/samtools/cram/testIGV1286.cram b/src/test/resources/htsjdk/samtools/cram/testIGV1286.cram new file mode 100644 index 0000000000000000000000000000000000000000..1f3e6fdef0106e3dae37bc22126ef07557595bf6 GIT binary patch literal 33017 zcmdSAWmr}1_V2&wR8qRTq&uV*4bmV=Hz?g9jdUX^Azgw3N=Zp~gG#s3Azf!K)_V3n zXaD!!&+od=8)*$m6$Fs0g^R0#oDLVaAV0gAvxyxD_{ZP_ 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UR:/STARK/databases/genomes/current/hg19.fa +@SQ SN:chr20 LN:63025520 M5:0dec9660ec1efaaf33281c0d5ea2560f UR:/STARK/databases/genomes/current/hg19.fa +@SQ SN:chr21 LN:48129895 M5:2979a6085bfe28e3ad6f552f361ed74d UR:/STARK/databases/genomes/current/hg19.fa +@SQ SN:chr22 LN:51304566 M5:a718acaa6135fdca8357d5bfe94211dd UR:/STARK/databases/genomes/current/hg19.fa +@SQ SN:chrM LN:16571 M5:d2ed829b8a1628d16cbeee88e88e39eb UR:/STARK/databases/genomes/current/hg19.fa +@SQ SN:chrX LN:155270560 M5:7e0e2e580297b7764e31dbc80c2540dd UR:/STARK/databases/genomes/current/hg19.fa +@SQ SN:chrY LN:59373566 M5:1e86411d73e6f00a10590f976be01623 UR:/STARK/databases/genomes/current/hg19.fa +@RG ID:1 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-1A6EF147 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-1D1A532C PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2BED613B PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2DFB3137 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2EDE9003 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2F408664 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-371D323C PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-3CDD0D7F PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-4B0C0FA1 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-51CB9B4 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-6514D4E8 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-654A89CA PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-7757D700 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-799CE28A PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-7C5762BA PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-C30A871 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-6811CC32 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-1A6EF147-54E84734 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-1D1A532C-26408A6E PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2BED613B-32686425 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2DFB3137-4AF997D4 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2EDE9003-7B672A6 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2F408664-8A1B60D PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-371D323C-392B6D82 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-3CDD0D7F-7F8745FE PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-4B0C0FA1-62697EA8 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-51CB9B4-5FA7132C PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-6514D4E8-5E27724F PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-654A89CA-2A5B938F PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-7757D700-29B03790 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-799CE28A-32328D0E PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-7C5762BA-637272BA PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-C30A871-546A7047 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-5E3F1AEB PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-1A6EF147-313C432 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-1D1A532C-44768E28 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2BED613B-7B719EDE PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2DFB3137-2E423B5D PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2EDE9003-54B41CD4 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2F408664-1978DD4A PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-371D323C-4FC732F5 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-3CDD0D7F-76C3C865 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-4B0C0FA1-495A019F PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-51CB9B4-17ED3450 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-6514D4E8-48930E57 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-654A89CA-6DD906EC PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-7757D700-6162AE67 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-799CE28A-6FACBBF0 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-7C5762BA-1C10D44A PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-C30A871-3C177F2B PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2138C620 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-1A6EF147-7F686190 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-1D1A532C-5CF1E1FB PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2BED613B-2CB81710 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2DFB3137-7C79ABE8 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2EDE9003-57DD1198 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-2F408664-50A18F81 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-371D323C-6B3D43BD PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-3CDD0D7F-2F2844ED PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-4B0C0FA1-2034B25A PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-51CB9B4-5B543B88 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-6514D4E8-78265C6D PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-654A89CA-5CC9CF6B PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-7757D700-51180468 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-799CE28A-39C48ED8 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-7C5762BA-5742D5A4 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@RG ID:1-C30A871-5C010636 PL:ILLUMINA PU:PU LB:001 SM:Sample4 +@PG ID:GATK IndelRealigner VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-14BBC0C6 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-19227BC7 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-22AB5829 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-29498544 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-2A21A11B VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-2C6A0607 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-338C3A86 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-45F9AEC4 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-46FB4A2C VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-481E8BEA VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-5B97BB23 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-60D26898 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-677C9008 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-6EFE6FCC VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-730EA918 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:bwa PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-10A23B79 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-2E16869 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-339BC180 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-39D1A348 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-54C178B5 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-6119380E PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-62EE1E19 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-63F133C0 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-66D30D89 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-69CB9F51 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-6B913448 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-6EF95606 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-7551147E PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-77A7B576 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-7868BF12 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-79A36CD1 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:samtools PN:samtools PP:bwa VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-1723A323 PN:samtools PP:bwa-54C178B5 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-1AF4308 PN:samtools PP:bwa-7551147E VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-24135F4F PN:samtools PP:bwa-339BC180 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-2B5EBFD6 PN:samtools PP:bwa-66D30D89 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-301BB32A PN:samtools PP:bwa-39D1A348 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-3068B2B7 PN:samtools PP:bwa-79A36CD1 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-35BA7A99 PN:samtools PP:bwa-2E16869 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-3A3576D2 PN:samtools PP:bwa-7868BF12 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-4DCBDFA5 PN:samtools PP:bwa-6EF95606 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T 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source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-14BBC0C6-5ABEC82C VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-19227BC7-79E52BA9 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-22AB5829-763C656 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-29498544-DDDB26D VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-2A21A11B-21E45DCD VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-2C6A0607-3D59D351 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-338C3A86-46CF07E VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-45F9AEC4-2F5ACD71 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-46FB4A2C-46C8F73E VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-481E8BEA-3E8CCE8 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-5B97BB23-E8328E7 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-60D26898-781BFB5D VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-677C9008-6D92A2AF VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-6EFE6FCC-4837A572 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-730EA918-52D9DA7F VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:bwa-D310894 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-10A23B79-2D055BAA PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-2E16869-1AA1CBB8 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-339BC180-1B8C5F0B PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-39D1A348-71C0F9C1 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-54C178B5-16966130 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-6119380E-5CC79558 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-62EE1E19-72A953CF PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-63F133C0-19A5D438 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-66D30D89-4F209372 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-69CB9F51-60742F5 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-6B913448-3D964ED6 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-6EF95606-73F94A7A PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-7551147E-339EB329 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-77A7B576-EACD58E PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-7868BF12-1DAD5EDF PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-79A36CD1-66C86ED7 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:samtools-2083FC92 PN:samtools PP:bwa-D310894 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-1723A323-1660A6ED PN:samtools PP:bwa-54C178B5-16966130 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-1AF4308-F625FE4 PN:samtools PP:bwa-7551147E-339EB329 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-24135F4F-3724AE2E PN:samtools PP:bwa-339BC180-1B8C5F0B VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-2B5EBFD6-6919380A PN:samtools PP:bwa-66D30D89-4F209372 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-301BB32A-2DA9D736 PN:samtools PP:bwa-39D1A348-71C0F9C1 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-3068B2B7-3D4CE48 PN:samtools PP:bwa-79A36CD1-66C86ED7 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o 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CL:/STARK/tools/samtools/current/bin/samtools view -O BAM -T /STARK/databases/genomes/current/hg19.fa -@ 1 /STARK/output/tmp/CAP_313626037/CAP_24866639/238239145.sam +@PG ID:samtools.82-75B89A55 PN:samtools PP:samtools.65-65C33187 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools view -O BAM -T /STARK/databases/genomes/current/hg19.fa -@ 1 /STARK/output/tmp/CAP_313626037/CAP_24866639/238239145.sam +@PG ID:samtools.83-22B41C9B PN:samtools PP:samtools.66-4D3D2BC7 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools view -O BAM -T /STARK/databases/genomes/current/hg19.fa -@ 1 /STARK/output/tmp/CAP_313626037/CAP_24866639/238239145.sam +@PG ID:samtools.84-6798D7F0 PN:samtools PP:samtools.67-3A2FF1B9 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools view -O BAM -T /STARK/databases/genomes/current/hg19.fa -@ 1 /STARK/output/tmp/CAP_313626037/CAP_24866639/238239145.sam +@PG ID:samtools.85-5CF03105 PN:samtools PP:samtools.68-3297BDC VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools view -O BAM -T /STARK/databases/genomes/current/hg19.fa -@ 1 /STARK/output/tmp/CAP_313626037/CAP_24866639/238239145.sam +@PG ID:samtools.86-4C0080D4 PN:samtools PP:samtools.69-541E6B86 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools view -O BAM -T /STARK/databases/genomes/current/hg19.fa -@ 1 /STARK/output/tmp/CAP_313626037/CAP_24866639/238239145.sam +@PG ID:samtools.87-7F3A656D PN:samtools PP:samtools.70-377577E3 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -o /STARK/output/tmp/CAP_313626037/CAP_24866639/2450817714 -l 0 -@ 1 - +@PG ID:samtools.88-51DD990B PN:samtools PP:samtools.71-53957FEC VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -o /STARK/output/tmp/CAP_313626037/CAP_24866639/2450817714 -l 0 -@ 1 - +@PG ID:samtools.89-69D8A83B PN:samtools PP:samtools.72-52835364 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -o /STARK/output/tmp/CAP_313626037/CAP_24866639/2450817714 -l 0 -@ 1 - 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ID:samtools.95-1FA5AFC0 PN:samtools PP:samtools.78-18A7818F VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -o /STARK/output/tmp/CAP_313626037/CAP_24866639/2450817714 -l 0 -@ 1 - +@PG ID:samtools.96-729CF9C PN:samtools PP:samtools.79-126409C9 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -o /STARK/output/tmp/CAP_313626037/CAP_24866639/2450817714 -l 0 -@ 1 - +@PG ID:samtools.97-3AD02F25 PN:samtools PP:samtools.80-5B2E073C VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -o /STARK/output/tmp/CAP_313626037/CAP_24866639/2450817714 -l 0 -@ 1 - +@PG ID:samtools.98-318C9054 PN:samtools PP:samtools.81-47664AC2 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -o /STARK/output/tmp/CAP_313626037/CAP_24866639/2450817714 -l 0 -@ 1 - +@PG ID:samtools.99-7360EF34 PN:samtools PP:samtools.82-75B89A55 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -o /STARK/output/tmp/CAP_313626037/CAP_24866639/2450817714 -l 0 -@ 1 - +@PG ID:samtools.100-46F6ECC0 PN:samtools PP:samtools.83-22B41C9B VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -o /STARK/output/tmp/CAP_313626037/CAP_24866639/2450817714 -l 0 -@ 1 - +@PG ID:samtools.101-5B91AB88 PN:samtools PP:samtools.84-6798D7F0 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -o /STARK/output/tmp/CAP_313626037/CAP_24866639/2450817714 -l 0 -@ 1 - +@PG ID:samtools.102-17EF5BE7 PN:samtools PP:samtools.85-5CF03105 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -o /STARK/output/tmp/CAP_313626037/CAP_24866639/2450817714 -l 0 -@ 1 - +@PG ID:samtools.103-470E7C64 PN:samtools PP:samtools.86-4C0080D4 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -o /STARK/output/tmp/CAP_313626037/CAP_24866639/2450817714 -l 0 -@ 1 - +@PG ID:GATK IndelRealigner-64F29E72 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-14BBC0C6-29F94F92 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-19227BC7-346B9387 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-22AB5829-770D0E7D VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-29498544-72AFCEE3 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-2A21A11B-6C2F0077 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-2C6A0607-707B27B3 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-338C3A86-7FEE044E VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-45F9AEC4-48FD7DBE VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-46FB4A2C-1D0F68F7 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-481E8BEA-2E7BF876 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-5B97BB23-617ADC33 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-60D26898-4A908F97 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-677C9008-4FFFB1E3 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-6EFE6FCC-20A5503A VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-730EA918-25664714 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] 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targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-14BBC0C6-333F23D5 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-19227BC7-18960831 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-22AB5829-30B8F06F VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-29498544-2542C30 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-2A21A11B-F0EFDCE VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-2C6A0607-6EEA77AF VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-338C3A86-360AB2E2 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-45F9AEC4-FBE0C3F VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-46FB4A2C-7ADEAE3 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-481E8BEA-631BBF27 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-5B97BB23-A8DCFF VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-60D26898-D0F140C VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-677C9008-7F88DA90 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-6EFE6FCC-24A765D3 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:GATK IndelRealigner-730EA918-2A884B73 VN:3.8-1-0-gf15c1c3ef CL:knownAlleles=[(RodBinding name=knownAlleles source=/STARK/databases/dbsnp/current/dbsnp.hg19.vcf.gz)] targetIntervals=/STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.for_realignment.RealignerTargetCreator.intervals LODThresholdForCleaning=2.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=2000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=50000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null +@PG ID:bwa-13ECB6A6 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-10A23B79-63DED2DA PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-2E16869-6196FDFE PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-339BC180-DA65A63 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-39D1A348-327A6CD PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-54C178B5-23C1CE14 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-6119380E-5B5A1007 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-62EE1E19-4FCDC145 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-63F133C0-180B4EC2 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-66D30D89-6E2B6B4E PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-69CB9F51-79CC7384 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-6B913448-57B7125A PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-6EF95606-5033B336 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-7551147E-170BFB5B PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-77A7B576-98DD882 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-7868BF12-427777CC PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:bwa-79A36CD1-47915364 PN:bwa VN:0.7.17-r1188 CL:/STARK/tools/bwa/current/bin/bwa mem -C -M -t 4 -R @RG\tID:1\tPL:ILLUMINA\tPU:PU\tLB:001\tSM:Sample4 /STARK/databases/genomes/current/hg19.fa /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R1.fastq.gz /STARK/output/results/RUN_TEST_920/Sample4/Sample4.R2.fastq.gz +@PG ID:samtools-46D9147E PN:samtools PP:bwa-13ECB6A6 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-1723A323-211962EB PN:samtools PP:bwa-54C178B5-23C1CE14 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-1AF4308-5E7FE860 PN:samtools PP:bwa-7551147E-170BFB5B VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-24135F4F-47E9B83A PN:samtools PP:bwa-339BC180-DA65A63 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-2B5EBFD6-730976B1 PN:samtools PP:bwa-66D30D89-6E2B6B4E VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-301BB32A-5CD85A01 PN:samtools PP:bwa-39D1A348-327A6CD VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-3068B2B7-1118ADD7 PN:samtools PP:bwa-79A36CD1-47915364 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-35BA7A99-601C84B2 PN:samtools PP:bwa-2E16869-6196FDFE VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-3A3576D2-7ABEAA91 PN:samtools PP:bwa-7868BF12-427777CC VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-4DCBDFA5-63D90E06 PN:samtools PP:bwa-6EF95606-5033B336 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-4FA9C888-57E8B6E7 PN:samtools PP:bwa-77A7B576-98DD882 VN:1.15.1 CL:/STARK/tools/samtools/current/bin/samtools sort -l 1 -O BAM -o /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.tmp -T /STARK/output/results/RUN_TEST_920/Sample4/Sample4.bwamem.compress.clipping.recalibration.realignment.sorting.bam.SAMTOOLS_PREFIX -@ 4 - +@PG ID:samtools-58EB2673-7CDFF940 PN:samtools 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