Samtools filtering

[jomaco]

Hi

I am trying to filter for those reads which are mapped but where the mate is unmapped.

I tried:

bsub "source samtools-0.1.18; samtools view -bt -f 8 F3H.fa.fai L2557F3H.sam > L2557F3H.bam"

This doesn't appear to have worked correctly.

I understand the bitwise flag codes to an extent but to be honest I've just been using the "plain english" picard tool (http://picard.sourceforge.net/explain-flags.html). I don't think I understand how to specify for these codes using the minus "-f" parameter.

Thanks

Jon

[swbarnes2]

Throw a -F 4 in there too, or you will get unmapped reads whose mate also did not map.

[jomaco]

Thanks. Very useful, I wasn't aware you could combine -F and -f