Filter SAM file for read pairs that align on same strand

Question

[kmyers2]

I want to filter a SAM file for read pairs that align to the same strand. That is for R1 and R2, I want the alignment to be either both on the forward strand (FF) or both on the reverse strand (RR).

I used samtools view -F 0x2 to exclude any instance where the pairs align correctly (FR) but it looks like it's still including some FR reads with short read 1 lengths.

How can I filter a SAM file to only give me read pairs that align on the same strand, either both reads on the forward strand or both reads on the reverse strand?

Answer 1

[Pierre Lindenbaum]

samtools view -e 'flag.paired && !flag.unmap && !flag.munmap && ((flag.reverse && flag.mreverse) || (!flag.reverse && !flag.mreverse))' in.bam