I have a duplicate level of approx 10% in a DNA resequencing experiment and my read depth drops off in a linear fashion towards approx 70% GC.
The assay is a SureSelect, done on an Illumina analyser.
I'm fairly confident that the poor coverage in highGC is due to some sort of PCR amplification bias, but was interested in looking specifically at the duplicate reads re their GC content.
How do I go about splitting the duplicates out of my bwa-aligned bam into their own bam so that I can look into this specifically?
Thanks, Chris
The assay is a SureSelect, done on an Illumina analyser.
I'm fairly confident that the poor coverage in highGC is due to some sort of PCR amplification bias, but was interested in looking specifically at the duplicate reads re their GC content.
How do I go about splitting the duplicates out of my bwa-aligned bam into their own bam so that I can look into this specifically?
Thanks, Chris
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