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SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Bcftools does the SNP calling. It can also concatenate BCF files, index BCFs for fast random access and convert BCF to VCF. In addition, bcftools can operate on some VCFs (e.g. calling SNPs from GL-tagged VCFs), but not for all VCFs; VCF to BCF conversion is not working at the moment, either.

Note: The Samtools 0.1.18 install includes the tabix and bgzip binaries from the Tabix-0.2.6 software as well as the bcftools program.

Environment Modules

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

System Variables

  • HPC_SAMTOOLS_DIR - installation directory
  • HPC_SAMTOOLS_BIN - executable directory