BCFtools

Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:

  • Samtools – Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
  • BCFtools – Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
  • HTSlib – A C library for reading/writing high-throughput sequencing data

Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of HSTlib so they can be built independently.

Software Details

Visit their website and view the support site

License: MIT/Expat License

Application: Bioinformatics

Platform: Linux-64

Citation: Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]

* Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011 Nov 1;27(21):2987-93. Epub 2011 Sep 8. [PMID: 21903627]

* Danecek P., Schiffels S., Durbin R. Multiallelic calling model in bcftools (-m), samtools.github.io/bcftools/call-m.pdf

* Li H. Improving SNP discovery by base alignment quality. Bioinformatics. 2011 Apr 15;27(8):1157-8. doi: 10.1093/bioinformatics/btr076. Epub 2011 Feb 13. [PMID: 21320865]

* Durbin R. Segregation based metric for variant call QC, samtools.github.io/bcftools/rd-SegBias.pdf

* Li H, Mathematical Notes on SAMtools Algorithms, www.broadinstitute.org/gatk/media/docs/Samtools.pdf