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. John -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
