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Old 09-09-2014, 07:04 AM   #5
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Location: Cambridge, UK

Join Date: May 2010
Posts: 311

Originally Posted by thh32 View Post
This would work if I wanted a SAM file output but I am aiming for a similar output to that provided with bowtie where you get a file of the reads that align to the indexed file and a seperate file for reads that dont align to the indexed file.

Is there a way to do this with BWA?
Untested, but it should work in bash:

bwa mem myIndex myReads.fq.gz \
| tee >(samtools view -Sh -f4 - > unmapped.sam) \
| tee >(samtools view -Sh -F4 - > mapped.sam) > /dev/null
This sends unmapped reads (-f4) to unmapped.sam and mapped reads (-F4) to mapped.sam. You could customize the samtools commands in the subshells to decide what goes in each file (e.g. by using -q options). In fact, while you are at it, I would convert to bam and sort the mapped reads.

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