samtools/bcftools 1.2

on GitHub

• new bcftools consensus command
• new bcftools annotate plugins: fixploidy, vcf2sex, tag2tag
• more features in bcftools convert command, amongst others new --hapsample function (thanks to Warren Kretzschmar @wkretzsch)
• support for complements in bcftools annotate --remove
• support for -i/-e filtering expressions in bcftools isec
• improved error reporting
• bcftools call
  • the default prior increased from -P 1e-3 to -P 1.1e-3, some clear calls were missed with default settings previously
  • support for the new symbolic allele <*>
  • support for -f GQ
  • bug fixes, such as: proper trimming of DPR tag with -c; the -A switch does not add back records removed by -v and the behaviour has been made consistent with -c and -m
• many bug fixes and improvements, such as
  • bug in filtering, FMT & INFO vs INFO & FMT
  • fixes in bcftools merge
  • filter update AN/AC with -S
  • isec outputs matching records for both VCFs in the Venn mode
  • annotate considers alleles when working with Number=A,R tags
  • new --set-id feature for annotate
  • convert can be used similarly to view

The bcftools-1.2.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.