[Samtools-announce] samtools/bcftools/htslib 1.0 released
From: John Marshall <jm18@sa...> - 2014-08-15 17:58:00
Major new versions of samtools and associated tools have been released. Significant changes include:
- support for CRAM, a sequence data file format with better compression than BAM
- support for BCF v2, a binary equivalent to the VCF format that is more flexible than the old BCF1
- bcftools has been split out from samtools as a fully-featured VCF/BCF manipulation toolkit
- much work on the variant calling algorithms
- replacement of samtools's SAM/BAM readers and writers with new implementations in htslib
- a more flexible API for writing programs using htslib's API rather than the old samtools bam.h (which will remain supported and usable for a while yet)
BCFtools has been significantly expanded to provide many tools for basic manipulation of VCF and BCF files. Both SAMtools and BCFtools now use HTSlib for their low-level SAM/BAM/CRAM and VCF/BCF file operations. Due to these reorganisations there are many small changes and improvements -- notably most tools automatically detect what kind of input files they have been provided with.
These releases can be found at http://www.htslib.org/. Development and source code of these projects are linked from that web site and can be found in various Git repositories under https://github.com/samtools. The web site at http://samtools.sourceforge.net contains information for the old 0.1.x samtools/bcftools releases which is still useful but needs some updating for the 1.0 release.
The http://www.htslib.org website will be updated over the coming days and weeks with new workflows and updated information from the old website. It has been a long time since the last samtools release -- we anticipate making more frequent samtools, bcftools, and htslib releases in future.