Thursday, September 25, 2014

Fwd: 1.1 releases of HTSlib, Samtools, and BCFtools available

Fwd: please follow footer link

FWD from a post by John Marshall
"New 1.1 versions of htslib, samtools, and bcftools have been released.  These are minor bug-fix releases, and include the following notable fixes and new functionality compared to 1.0:

* Samtools fixmate and flagstat now consider supplementary reads
* Sorting BAM files with thousands of reference contigs now completes in a reasonable amount of time
* Fixed samtools idxstats when displaying statistics from indices generated by samtools 0.1.x
* Fixed samtools calmd memory leak
* Samtools fixmate now only adds a template cigar tag (ct:Z) when requested with -c, and never adds it repeatedly
* Regularised script #! directives as #!/usr/bin/env perl etc
* Fixed DPR annotation in samtools mpileup
* New bcftools convert and plugin commands and annotate --rename-chrs option
* BCFtools norm performance is improved and now averages QUALs and accumulates IDs and FILTERs
* Improved bcftools filter expressions, query support for IUPAC ambiguity codes, and annotate support for genotype fields
* Plugins for bcftools have now moved from annotate to the new plugin command

These releases can be found at . Development and source code of these projects are linked from that web site and can be found in various Git repositories under . Updates to the web site are ongoing. In particular, we have recently added a sample CRAM workflow: see .

Installing the tools will also install manual pages for them. Once installed, you should be able to use "man bcftools" etc at your command line to find details of new commands and functionality. Manual pages are also available online at and these will soon be updated to reflect the 1.1 release.