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Wednesday, July 23, 2014

Sort BAM File in Samtools

Samtools does a host of useful operations for .bam files.  One such operation is sorting.  Below is a simple example script to show how to use samtools to sort an unsorted BAM file.

This script will sort the unsorted.bam using 8 threads that allocates 12G of memory per thread.  The resulting sorted .bam file will be called sorted.bam.

To confirm a .bam file is sorted, check the header (samtools view -H sorted.bam) for the line:

Additionally, here is the usage information for Samtools sort:

Usage:   samtools sort [options]

Options: -n        sort by read name
         -f        use as full file name instead of prefix
         -o        final output to stdout
         -l INT    compression level, from 0 to 9 [-1]
         -@ INT    number of sorting and compression threads [1]
         -m INT    max memory per thread; suffix K/M/G recognized [768M]

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