1.16

Download the source code here: bcftools-1.16.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 plugin bcftools +variant-distance to annotate records with distance to the nearest variant (#1690)

Changes affecting the whole of bcftools, or multiple commands:

• The -i/-e filtering expressions

  • Added support for querying of multiple filters, for example -i 'FILTER="A;B"' can be used to select sites with two filters "A" and "B" set. See the documentation for more examples.

  • Added modulo arithmetic operator

Changes affecting specific commands:

• bcftools annotate

  • A bug introduced in 1.14 caused that records with INFO/END annotation would incorrectly trigger -c ~INFO/END mode of comparison even when not explicitly requested, which would result in not transferring the annotation from a tab-delimited file (#1733)

• bcftools merge

  • New -m snp-ins-del switch to merge SNVs, insertions and deletions separately (#1704)

• bcftools mpileup

  • New NMBZ annotation for Mann-Whitney U-z test on number of mismatches within supporting reads

  • Suppress the output of MQSBZ and FS annotations in absence of alternate allele

• bcftools +scatter

  • Fix erroneous addition of duplicate PG lines

• bcftools +setGT

  • Custom genotypes (e.g. -n c:1/1) now correctly override ploidy