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@jmarshall jmarshall released this 04 Feb 10:24
· 2048 commits to develop since this release
1.2
3529081
  • new bcftools consensus command
  • new bcftools annotate plugins: fixploidy, vcf2sex, tag2tag
  • more features in bcftools convert command, amongst others new --hapsample function (thanks to Warren Kretzschmar @wkretzsch)
  • support for complements in bcftools annotate --remove
  • support for -i/-e filtering expressions in bcftools isec
  • improved error reporting
  • bcftools call
    • the default prior increased from -P 1e-3 to -P 1.1e-3, some clear calls were missed with default settings previously
    • support for the new symbolic allele <*>
    • support for -f GQ
    • bug fixes, such as: proper trimming of DPR tag with -c; the -A switch does not add back records removed by -v and the behaviour has been made consistent with -c and -m
  • many bug fixes and improvements, such as
    • bug in filtering, FMT & INFO vs INFO & FMT
    • fixes in bcftools merge
    • filter update AN/AC with -S
    • isec outputs matching records for both VCFs in the Venn mode
    • annotate considers alleles when working with Number=A,R tags
    • new --set-id feature for annotate
    • convert can be used similarly to view

The bcftools-1.2.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.

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