Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

PrintReads for Pair-ended Reads

maramara Posts: 10Member

Extracting reads from a BAM file using PrintReads will give only the reads at a given loci (and not its pair). Is there a way to extract reads covering a certain locus in addition to its matched pair?

Thank you!

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