I have paired-end mapped reads (using bbmap) that I would like to separate based on the orientation of the read pairs. I see pairs as being able to have the following orientations:
LR: --> <--
LL or RR: --> --> or <-- <--
RL: <-- -->
I've managed to separate the reads in two, namely LR and one with the others ("discordant") using samtools:
samtools view -b infile.bam -F 1294 > outfile.bam
Which I picked up here , but am not too sure about... In IGV I can colour these discordant reads according to 'pair orientation'. I can see that they group together according to read orientation in clearly defined genomic positions.
But I have no idea how to split them based on orientation from here...
I tried several options, including a tool in the Jvarkit (unable to complete
make of BioAlcidae so could not run) and other custom scripts that did not work due being dependent on older versions of samtools/htslib...
I hope someone can help me from here - thanks! ^@^