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Forum: Bioinformatics 10-10-2013, 11:26 AM
Replies: 0
Views: 2,578
Posted By H_Peckham
Secondary Alignments with BWA-MEM

When I have split reads originating from repetitive sequences I must use the -a flag to get the secondary alignments. The problem with this is that with the -a flag there can be multiple secondary...
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