1.15.1

Download the source code here: bcftools-1.15.1.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.)

• bcftools annotate

  • New -H, --header-line convenience option to pass a header line on command line, this complements the existing -h, --header-lines option which requires a file with header lines

• bcftools csq

  • A list of consequence types supported by bcftools csq has been added to the manual page. (#1671)

• bcftools +fill-tags

  • Extend generalized functions so that FORMAT tags can be filled as well, for example:

    bcftools +fill-tags in.bcf -o out.bcf -- -t 'FORMAT/DP:1=int(smpl_sum(FORMAT/AD))'

  • Allow multiple custom functions in a single run. Previously the program would silently go with the last one, assigning the same values to all (#1684)

• bcftools norm

  • Fix an assertion failure triggered when a faulty VCF file with a '-' character in the REF allele was used with bcftools norm --atomize. This option now checks that the REF allele only includes the allowed characters A, C, G, T and N. (#1668)

  • Fix the loss of phasing in half-missing genotypes in variant atomization (#1689)

• bcftools roh

  • Fix a bug that could result in an endless loop or incorrect AF estimate when missing genotypes are present and the --estimate-AF - option was used (#1687)

• bcftools +split-vep

  • VEP fields with characters disallowed in VCF tag names by the specification (such as - in M-CAP) couldn't be queried. This has been fixed, the program now sanitizes the field names, replacing invalid characters with underscore (#1686)