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.
Program Location
/usr/local/samtools/
The easiest way to add samtools, bcftools and the miscellaneous tools to your path is by using the modules commands as in the example below:
[user@helix]$ module avail samtools (see what versions are available) ------------------- /usr/local/Modules/3.2.9/modulefiles ------------------- samtools/0.1.12a samtools/0.1.15 samtools/0.1.18(default) samtools/0.1.13 samtools/0.1.17 [user@helix]$ module load samtools (load the default version) [user@helix]$ module list (see what version is loaded) Currently Loaded Modulefiles: 1) samtools/0.1.18 [user@helix]$ module unload samtools (unload this version) [user@helix]$ module load samtools/0.1.15 (load a specific version) [user@helix]$ module list Currently Loaded Modulefiles: 1) samtools/0.1.15
Sample Session on Helix
SAMtools sample files can be copied from:
/usr/local/samtools/examplesto your own /data/user area.
% module load samtools % cd /home/user/samtools/run1 % samtools faidx ex1.fa # index the reference FASTA % samtools import ex1.fa.fai ex1.sam.gz ex1.bam # SAM->BAM % samtools index ex1.bam # index BAM % samtools tview ex1.bam ex1.fa # view alignment % samtools pileup -cf ex1.fa ex1.bam # pileup and consensus
