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@daviesrob daviesrob released this 28 Sep 16:54
· 1347 commits to develop since this release
1.6
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daviesrob
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  • New sort command.

  • New options added to the consensus command. Note that the -i, --iupac option has been renamed to -I, --iupac, in favor of the standard -i, --include.

  • Filtering expressions (-i/-e): support for GT=<type> expressions and for lists and ranges (#639) - see the man page for details.

  • csq: relax some GFF3 parsing restrictions to enable using Ensembl GFF3 files for plants (#667)

  • stats: add further documentation to output stats files (#316) and include haploid counts in per-sample output (#671).

  • plot-vcfstats: further fixes for Python3 (@nsoranzo, #645, #666).

  • query bugfix (#632)

  • +setGT plugin: new option to set genotypes based on a two-tailed binomial distribution test. Also, allow combining -i/-e with -t q.

  • mpileup: fix typo (#636)

  • convert --gvcf2vcf bugfix (#641)

  • +mendelian: recognize some mendelian inconsistencies that were being missed (@oronnavon, #660), also add support for multiallelic sites and sex chromosomes.

The bcftools-1.6.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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