Split bwa mem for MergeBamAlignment
Hi team,
Struggling on how to split bwa mem output into mapped vs unmapped to use with Picards MergeBamAlignment (to get MQ values). Seems it doesn't like having the same read ids which means you have to be careful where one pair is unmapped while the other one is mapped and vice versa. Can't seem to work out the correct set of -f and -F from samtools to get it to work.
Thanking you in advance.
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