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CSB5 / lofreq

LoFreq Star: Sensitive variant calling from sequencing data
http://csb5.github.io/lofreq/
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Confirm that --max-depth is per-base coverage #97

Closed rspreafico-vir closed 4 years ago

rspreafico-vir commented 4 years ago

Hi there,

just wanted to confirm that --max-depth caps coverage at per-base level, as opposed to read level. I have a dataset with pretty uneven coverage (by design, because of the way the assay works) and some of the low-coverage sites seem not to get as much coverage as I anticipated, and I wonder whether that is because I am capping depth.

Thank you!

andreas-wilm commented 4 years ago

Hi Roberto, yes correct, it's base level coverage, however, after read level filtering.

rspreafico-vir commented 4 years ago

Thank you Andreas!