1.15

Download the source code here: bcftools-1.15.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)

• New bcftools head subcommand for conveniently displaying the headers of a VCF or BCF file. Without any options, this is equivalent to bcftools view --header-only --no-version but more succinct and memorable.

• The -T, --targets-file option had the following bug originating in HTSlib code: when an uncompressed file with multiple columns CHR,POS,REF was provided, the REF would be interpreted as 0 gigabases (#1598)

Changes affecting specific commands:

• bcftools annotate

  • In addition to --rename-annots, which requires a file with name mappings, it is now possible to do the same on the command line -c NEW_TAG:=OLD_TAG

  • Add new option --min-overlap which allows to specify the minimum required overlap of intersecting regions

  • Allow to transfer ALT from VCF with or without replacement using:
    bcftools annotate -a annots.vcf.gz -c ALT file.vcf.gz
bcftools annotate -a annots.vcf.gz -c +ALT file.vcf.gz

• bcftools convert

  • Revamp of --gensample, --hapsample and --haplegendsample family of options which includes the following changes:

  • New --3N6 option to output/input the new version of the .gen file format, see https://www.cog-genomics.org/plink/2.0/formats#gen

  • Deprecate the --chrom option in favor of --3N6. A simple cut command can be used to convert from the new 3*M+6 column format to the format printed with --chrom (cut -d' ' -f1,3-).

  • The CHROM:POS_REF_ALT IDs which are used to detect strand swaps are required and must appear either in the "SNP ID" column or the "rsID" column. The column is autodetected for --gensample2vcf, can be the first or the second for --hapsample2vcf (depending on whether the --vcf-ids option is given), must be the first for --haplegendsample2vcf.

• bcftools csq

  • Allow GFF files with phase column unset

• bcftools filter

  • New --mask, --mask-file and --mask-overlap options to soft filter variants in regions (#1635)

• bcftools +fixref

  • The -m id option now works also for non-dbSNP ids, i.e. not just rsINT

  • New -m flip-all mode for flipping all sites, including ambiguous A/T and C/G sites

• bcftools isec

  • Prevent segfault on sites filtered with -i/-e in all files (#1632)

• bcftools mpileup

  • More flexible read filtering using the options:
    --ls, --skip-all-set .. skip reads with all of the FLAG bits set
    --ns, --skip-any-set .. skip reads with any of the FLAG bits set
    --lu, --skip-all-unset .. skip reads with all of the FLAG bits unset
    --nu, --skip-any-unset .. skip reads with any of the FLAG bits unset

    The existing synonymous options will continue to function but their use is discouraged:

    --rf, --incl-flags STR|INT Required flags: skip reads with mask bits unset
    --ff, --excl-flags STR|INT Filter flags: skip reads with mask bits set

• bcftools query

  • Make the --samples and --samples-file options work also in the --list-samples mode. Add a new --force-samples option which allows to proceed even when some of the requested samples are not present in the VCF (#1631)

• bcftools +setGT

  • Fix a bug in -t q -e EXPR logic applied on FORMAT fields, sites with all samples failing the expression EXPR were incorrectly skipped. This problem affected only the use of -e logic, not the -i expressions (#1607)

• bcftools sort

  • make use of the TMPDIR environment variable when defined

• bcftools +trio-dnm2

  • The --use-NAIVE mode now also adds the de novo allele in FORMAT/VA