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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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when input bam , nedd to remove or mark duplicates filres? #48

Closed YangLeng90 closed 2 years ago

YangLeng90 commented 2 years ago

when input bam , Does it need to remove or mark duplicates first?

dariober commented 2 years ago

Hi- Marking duplicates is not a requirement, but in most cases it is preferable to mark them. snp-pileup, one of the tools behind cnv_facets will ignore reads marked as duplicate.

I close the issue now but feel free to re-open.