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@daviesrob daviesrob released this 12 Feb 17:12
· 1216 commits to develop since this release
1.7
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daviesrob
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  • -i, -e filtering: Major revamp, improved filtering by FORMAT fields and missing values. New GT=ref,alt,mis etc keywords, check the documentation for details.

  • query: Only matching expression are printed when both the -f and -i/-e expressions contain genotype fields. Note that this changes the original behaviour. Previously all samples were output when one matching sample was found. This functionality can be achieved by pre-filtering with view and then streaming to query. Compare
    bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]' -i'GT="alt"' file.bcf
    and
    bcftools view -i'GT="alt"' file.bcf -Ou | bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]'

  • annotate: New -k, --keep-sites option

  • consensus: Fix --iupac-codes output

  • csq: Homs always considered phased and other fixes

  • norm: Make -c none work and remove query -c

  • roh: Fix errors in the RG output

  • stats: Allow IUPAC ambiguity codes in the reference file; report the number of missing genotypes

  • +fill-tags: Add ExcHet annotation

  • +setGt: Fix bug in binom.test calculation, previously it worked only for nAlt<nRef!

  • +split: New plugin to split a multi-sample file into single-sample files in one go

  • Improve python3 compatibility in plotting scripts

The bcftools-1.7.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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