We are wanting to know how best to combine SE and PE reads for SNP calling. There is a prior query on this from 2013 at the following URL:
That was from some time ago, so what is the latest understanding regarding this and is there a consistent way to combine the SNP calling that makes sense?
The fact that the MAPQ score upper limit for PE is 60 with SE being 37; is this quantitatively consistent with the increased accuracy of mapping with PE reads when it comes to filtering?
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