Hi All
I target a highly homologous target region of about 300 Kb. I have an
bwa-aligned BAM file that is not marked for duplicates. When I use Picard to
CollectHsMetrics, I find that about 15% of the region is not covered (using
PCT_TARGET_BASES_2X). As far as I know all my regions are covered, which I
checked this with complementary tools such as CallableLoci from GATK.
My question is does Picard ignore Low/Zero MQ reads while estimating different
metrics?
Thanks
Siva
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