samtools/bcftools 1.3

on GitHub

• bcftools call has new options --ploidy and --ploidy-file to make handling sample ploidy easier. See man page for details.
• stats: -i/-e short options changed to -I/-E to be consistent with the filtering -i/-e (--include/--exclude) options used in other tools.
• general --threads option to control the number of output compression threads used when outputting compressed VCF or BCF.
• cnv and polysomy: new commands for detecting CNVs, aneuploidy, and contamination from SNP genotyping data.
• various new options, plugins, and bug fixes, including #84, #201, #204, #205, #208, #211, #222, #225, #242, #243, #249, #282, #285, #289, #302, #311, #318, #336, and #338.

The bcftools-1.3.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing some generated files.