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@valeriuo valeriuo released this 21 Jun 11:56
· 1340 commits to master since this release
1.5
04608ff

  • 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.

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