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Old 12-09-2016, 06:27 AM   #8
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
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Oh! Yes, technically bs.sh is not part of the BBMap package. Rather, it gets produced by BBMap if you add the flag "bs=bs.sh", because it is a custom script specific to the name of the sam/bam file BBMap produced. bs.sh simply calls Samtools with the correct (or, in the above case, apparently incorrect) commands to produce a sorted, indexed bam file.

Generally, you do this:

Code:
bbmap.sh in=reads.fq.gz out=mapped.bam bs=bs.sh; sh bs.sh
That produces sorted_mapped.bam and sorted_mapped.bam.bai.

Last edited by Brian Bushnell; 12-09-2016 at 09:06 AM.
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