Manual pages

Documentation for BCFtools, SAMtools, and HTSlib’s utilities is available by using man command on the command line. The manual pages for several releases are also included below — be sure to consult the documentation for the release you are using.

File formats

SAMtools conforms to the specifications produced by the GA4GH File Formats working group. Details of the current specifications are available on the hts-specs page.

HTSlib also includes brief manual pages outlining aspects of several of the more important file formats. These are available via man format on the command line or here on the web site:

Algorithms

Benchmarks

Publications

File formats

The introduction of the SAM/BAM format and the samtools command line tool:

Extension of the SAM/BAM format to support de novo assemblies:

The introduction of the CRAM format:

The introduction of the VCF format:

Calling and analysis

The original mpileup calling algorithm plus mathematical notes (mpileup/bcftools call -c):

Mathematical notes for the updated multiallelic calling model (mpileup/bcftools call -m):

Hidden Markov model for detecting runs of homozygosity (bcftools roh):

Copy number variation/aneuploidy calling from microarray data (bcftools cnv/bcftools polysomy):

Haplotype-aware calling of variant consequences (bcftools csq):

Other

Base alignment quality (BAQ) method improve SNP calling around INDELs:

Segregation based QC metric originally implemented in SGA: