Does genomecov count marked duplicates?

[Dan Sun]

Hi,

I have a question about genomecov. Does genomecov count duplicate reads after marking (not removing) them using software like Picard? I hope it does not..

Thanks!

[Aaron Quinlan]

Hi Dan,

I counts every aligned record that you provide it.  To filter out duplicates, you could use samtools to exclude duplicates and pipe the results into genomecov (bam format).

I hope this helps.

Aaron

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[Dan Sun]

Thanks! Since more and more people choose to mark duplicates instead, I think it would be more powerful to include the recognition of marked duplicates

Dan