Skip to content

1.7
Compare
Choose a tag to compare
@daviesrob daviesrob released this 12 Feb 17:12
· 1289 commits to develop since this release
1.7
This tag was signed with the committer’s verified signature.
daviesrob
GPG key ID: 1ECBE5BA15C64CCC
Learn about vigilant mode.
33b14f1

  • -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.

Assets 3
Loading