Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires sorted output from BWA-MEM (use -M and -x parameter) or NGMLR with the optional SAM attributes enabled! If you experience problems or have suggestions please contact: [email protected]
Please see our github wiki for more information (https://github.com/fritzsedlazeck/Sniffles/wiki)
wget https://github.com/fritzsedlazeck/Sniffles/archive/master.tar.gz -O Sniffles.tar.gz tar xzvf Sniffles.tar.gz cd Sniffles-master/ mkdir -p build/ cd build/ cmake .. make cd ../bin/sniffles* ./sniffles
Note Mac users often have to provide parameters to the cmake command:
cmake -D CMAKE_C_COMPILER=/opt/local/bin/gcc-mp-4.7 -D CMAKE_CXX_COMPILER=/opt/local/bin/g++-mp-4.7 ..
Sniffles performs best with the mappings of NGMLR our novel long read mapping method. Please see: https://github.com/philres/ngmlr
Please see and cite our paper: https://www.nature.com/articles/s41592-018-0001-7
Accurate and fast detection of complex and nested structural variations using long read technologies Biological Data Science, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 26 - 29.10.2016
NGMLR: Highly accurate read mapping of third generation sequencing reads for improved structural variation analysis Genome Informatics 2016, Wellcome Genome Campus Conference Centre, Hinxton, Cambridge, UK, 19.09.-2.09.2016
We provide the NGMLR aligned reads and the Sniffles calls for the data sets used:
Arabidopsis trio:
Genome in the Bottle trio:
-
Mappings: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/PacBio_MtSinai_NIST/Baylor_NGMLR_bam_GRCh37/ .
-
SV calls: http://labshare.cshl.edu/shares/schatzlab/www-data/fsedlaze/Sniffles/GiaB/
NA12878:
SKBR3: