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jsh58 / Genrich

Detecting sites of genomic enrichment
MIT License
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Pre-marked duplicate read removal #48

Closed Maarten-vd-Sande closed 4 years ago

Maarten-vd-Sande commented 4 years ago

I quickly scanned the source code, but it seems that genrich includes all reads, and ignores whether a read is a duplicate or not:

read is PCR or optical duplicate (0x400)

Am I correct in my understanding? Is it possible to use this flag instead of checking again what are duplicates?

jsh58 commented 4 years ago

Thanks for the question. Genrich does not analyze alignments already marked as duplicates. It also skips supplementary and low quality alignments ("not passing filters"). In verbose mode, these will show up in the counts.

Maarten-vd-Sande commented 4 years ago

Thanks for answering so fast!