Hi team,
Struggling 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.
Thanking you in advance.
Struggling 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.
Thanking you in advance.
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