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class: s:SoftwareSourceCode
s:name: "samtools"
s:about: >
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)
and HTSlib (A C library for reading/writing high-throughput sequencing data).
s:url: http://www.htslib.org/
s:codeRepository: https://github.com/samtools/samtools.git
s:license:
- https://opensource.org/licenses/MIT
- https://opensource.org/licenses/BSD-3-Clause
s:targetProduct:
class: s:SoftwareApplication
s:softwareVersion: "1.2-242-4d56437"
s:applicationCategory: "commandline tool"
s:programmingLanguage: "C, Perl"
s:publication:
- class: s:ScholarlyArticle
id: http://dx.doi.org/10.1093/bioinformatics/btr509
s:name: "(Li, 2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics."
s:url: http://www.ncbi.nlm.nih.gov/pubmed/21903627
- class: s:ScholarlyArticle
id: http://dx.doi.org/10.1093/bioinformatics/btr076
s:name: "(Li, 2011) Improving SNP discovery by base alignment quality. Bioinformatics."
s:url: http://www.ncbi.nlm.nih.gov/pubmed/21320865
- class: s:ScholarlyArticle
id: http://dx.doi.org/10.1093/bioinformatics/btp352
s:name: "(Li et al., 2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics."
s:url: http://www.ncbi.nlm.nih.gov/pubmed/19505943
s:discussionUrl:
- https://lists.sourceforge.net/lists/listinfo/samtools-help
- https://lists.sourceforge.net/lists/listinfo/samtools-devel
s:creator:
- class: s:Organization
s:name: "Sanger Institute"
s:member:
- class: s:Person
s:name: "Heng Li"
s:description: "wrote most of the initial source codes of SAMtools and various converters."
- class: s:Organization
s:name: "Broad Institute"
s:member:
- class: s:Person
s:name: "Bob Handsaker"
s:description: |
A major contributor to the
SAM/BAM specification. He designed and implemented the BGZF format, the
underlying indexable compression format for the BAM format. BGZF does
not support arithmetic between file offsets.
- class: s:Organization
s:name: "Beijing Genome Institute"
s:member:
- class: s:Person
s:name: "Jue Ruan"
s:description: |
Designed and implemented the
RAZF format, an alternative indexable compression format. RAZF is no longer
used by or provided with SAMtools. Source code remains available in older
SAMtools 0.1.x releases and from the standalone branch in the repository.
- class: s:Person
s:name: "Colin Hercus"
s:description: "updated novo2sam.pl to support gapped alignment by novoalign."
- class: s:Person
s:name: "Petr Danecek"
s:description: "contributed the header parsing library sam_header.c and sam2vcf.pl script."
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