samtools/bcftools 1.5

on GitHub

• Added autoconf support to bcftools. See INSTALL for more details.

• norm: Make norm case insensitive (#601). Trim the reference allele (#602).

• mpileup: fix for misreported indel depths for reads containing adjacent indels (3c1205c).

• plot-vcfstats: Open stats file in text mode, not binary (#618).

• fixref plugin: Allow multiallelic sites in the -i, --use-id reference. Also flip genotypes, not just REF/ALT!

• merge: fix gVCF merge bug when last record on a chromosome opened a gVCF block (#616)

• New options added to the ROH plotting script.

• consensus: Properly flush chain info (#606, thanks to @krooijers).

• New +prune plugin for pruning sites by LD (R2) or maximum number of records within a window.

• New N_MISSING, F_MISSING (number and fraction missing) filtering expressions.

• Fix HMM initialization in roh when snapshots are used in multiple chromosome VCF.

• Fix buffer overflow (#607) in filter.

The bcftools-1.5.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.