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@daviesrob daviesrob released this 06 Dec 17:18
· 907 commits to develop since this release
1.10
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daviesrob
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The bcftools-1.10.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.

  • Numerous bug fixes, usability improvements and sanity checks were added to prevent common user errors.

  • The -r, --regions (and -R, --regions-file) option should never create unsorted VCFs or duplicates records again. This also fixes rare cases where a spanning deletion makes a subsequent record invisible to bcftools isec and other commands.

  • Additions to filtering and formatting expressions

    • support for the spanning deletion alternate allele (ALT=*)

    • new ILEN filtering expression to be able to filter by indel length

    • new MEAN, MEDIAN, MODE, STDEV, phred filtering functions

    • new formatting expression %PBINOM (phred-scaled binomial probability), %INFO (the whole INFO column), %FORMAT (the whole FORMAT column), %END (end position of the REF allele), %END0 (0-based end position of the REF allele), %MASK (with multiple files indicates the presence of the site in other files)

  • New plugins

    • +gvcfz: compress gVCF file by resizing gVCF blocks according to specified criteria

    • +indel-stats: collect various indel-specific statistics

    • +parental-origin: determine parental origin of a CNV region

    • +remove-overlaps: remove overlapping variants.

    • +split-vep: query structured annotations such INFO/CSQ created by bcftools/csq or VEP

    • +trio-dnm: screen variants for possible de-novo mutations in trios

  • annotate

    • new -l, --merge-logic option for combining multiple overlapping regions

  • call

    • new bcftools call -G, --group-samples option which allows grouping samples into populations and applying the HWE assumption within but not across the groups.

  • csq

    • significant reduction of memory usage in the local -l mode for VCFs with thousands of samples and 20% reduction in the non-local haplotype-aware mode.

    • fixes a small memory leak and formatting issue in FORMAT/BCSQ at sites with many consequences

    • do not print protein sequence of start_lost events

    • support for "start_retained" consequence

    • support for symbolic insertions (ALT="<INS...>"), "feature_elongation" consequence

    • new -b, --brief-predictions option to output abbreviated protein predictions.

  • concat

    • the --naive command now checks header compatibility when concatenating multiple files.

  • consensus

    • add a new -H, --haplotype 1pIu/2pIu feature to output first/second allele for phased genotypes and the IUPAC code for unphased genotypes

    • new -p, --prefix option to add a prefix to sequence names on output

  • +contrast

    • added support for Fisher's test probability and other annotations

  • +fill-from-fasta

    • new -N, --replace-non-ACGTN option

  • +dosage

    • fix some serious bugs in dosage calculation

  • +fill-tags

    • extended to perform simple on-the-fly calculations such as calculating INFO/DP from FORMAT/DP.

  • merge

    • add support for merging FORMAT strings

    • bug fixed in gVCF merging

  • mpileup

    • a new optional SCR annotation for the number of soft-clipped reads

  • reheader

    • new -f, --fai option for updating contig lines in the VCF header

  • +trio-stats

    • extend output to include DNM homs and recurrent DNMs

  • VariantKey support

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