Samtools¶

Description¶

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that: Is flexible enough to store all the alignment information generated by various alignment programs; Is simple enough to be easily generated by alignment programs or converted from existing alignment formats; Is compact in file size; Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory; Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Note: load htslib module for tabix, htsfile, and bgzip utilities. * BAM_ROOT - standard samtools variable for installation directory

Environment Modules¶

Run module spider samtools to find out what environment modules are available for this application.

Environment Variables¶

HPC_SAMTOOLS_DIR - installation directory
HPC_SAMTOOLS_BIN - executable directory
HPC_SAMTOOLS_INC - includes directory

Categories¶

biology, ngs, sequencing