Is there an easy & robust way to extract from a mapping bam file all the read pairs where both ends mapped, but to different reference pieces?
I had thought it might be possible using:
samtools view -F (or -f) <some flag>
but I can't figure out exactly what flag to use. Is there a bit for read pairs mapping to different reference pieces?
I had thought it might be possible using:
samtools view -F (or -f) <some flag>
but I can't figure out exactly what flag to use. Is there a bit for read pairs mapping to different reference pieces?
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