BWA option for FR sens only

Question

[Picasa]

Hi,

I am looking to bwa mem to map my reads.

However, I would like to keep only the real Forward-reverse paired end and to discard any weird sens (FF, RR, RF).

Is there any option in bwa to do this ?

Thanks

[Medhat]

maybe align them first then extract them using samtools view -hf 0x2 alignments.bam

[ATpoint]

Filtering by flag is a good idea. In case you need the flag concept explained, check the SAM format specifications and also this website, which can decode a flag:

Bitwise Flag explained

[WouterDeCoster]

You could also pipe bwa directly into samtools view, avoiding intermediate files.