bwa mem report only matches

[jsved]

Trivial question? - when aligning raw reads from a large file to a small reference sequence and 99.99..% of reads are non matches, with Flag 4, is there a flag to set to report only matches. Thanks, John

[dschika]

Have a look at:
https://www.biostars.org/p/56246/

[jsved]

Thanks for the suggestion. Unfortunately it does not solve the problem of producing a 40Gb .sam file when only 1Mb of it is useful. It seems to make my computer heavier.

[dschika]

Have you tried piping bwa mem output into samtools? Something like:

bwa mem [your options] | samtools view -SF 4 - > output.sam

[Brian Bushnell]

Also, BBMap has an "outm" flag, which will retain only mapped reads, but keep pairs together (if either one was mapped). For example:

bbmap.sh ref=reference.fa in1=r1.fq in2=r2.fq outm=mapped.sam

[jsved]

Many thanks for both the samtools and BBMap suggestions. I had not heard of BBMap, but was extremely impressed at its speed and the way outm worked.