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Samtools: Difference between revisions
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Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: | 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 | *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 | *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 | *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 htslib so they can be built independently. | Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently. | ||
Note: This page does not cover all features of SAMtools. Please refer to http://www.htslib.org/doc/samtools.html for the complete list of all subtools. | Note: This page does not cover all features of SAMtools. Please refer to [http://www.htslib.org/doc/samtools.html] for the complete list of all subtools. | ||