Index of /examples/bioinformatics/samtools

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Samtools package example

Samtools is by far a very rich software program that provides many different sets of utilities to process high throughput sequence data. This example page would not be possible to cover all of them, but only serve as a sample/template of how to use it on SCC.

Samtools consists of three separate parts:

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