- Description
- SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM/BAM format.
- Modulefile
samtools- Documentation
- SAMtools homepage
- Usage
- Here is an example of creating an index file
sorted.bam.bai for the sorted.bam file:
$ module load samtools
$ samtools index sorted.bam
- Here is an example how one could link their code compiled with GCC against the appropriate SAMtools 0.1.x library:
$ module load gcc samtools/gcc
$ gcc <compiler commands> -I$SAMTOOLS/include -L$SAMTOOLS/lib -lbam