SAM: extract both pairs where at least one pair mapped

[spabinger]

Hi,

I want to extract both pairs from a SAM file where at least one pair mapped (or both). The ideal solution would be to get 2 fastq files where either both reads mapped, or only one pair mapped and the unmapped pair is also extracted.

I tried various flag combination with "samtools view" but didn't get the desired result. So far I know how to get all mapped reads, but the unmapped second pair is missing.

Thanks, Stephan

[Kennels]

Not sure if this would help. There's a tool here:

http://picard.sourceforge.net/explain-flags.html

that gives you the flag for whatever you're after.

[spabinger]

Thanks. I've already tried that, but I'm not sure which flags to use.

Stephan

[swbarnes2]

samtools view -F 12 whatever.bam

should get all the reads where both mapped.

samtools view -f 4 -F 8 whatever.bam

should get all the reads that did not map, but whose mate mapped

samtools view -f 8 -F 4 whatever.bam

Should get all the reads that mapped, but whose mates did not.

Or, do

samtools view -f 12 whatever.bam

To get all the reads where neither one mapped, then collect all those read names, and get everything not in that list.

[spabinger]

Thanks! I just tried it and it works perfectly.

Stephan