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brentp / mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
MIT License
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Feature Request: Max depth of a feature/gene #108

Open lemetrec opened 4 years ago

lemetrec commented 4 years ago

Hi there!

I was curious if you are planning to add an option to get the max depth within the window of a feature/gene from the BED file? Unless I am not seeing it.

Thank you! Christophe

Biojenifer commented 4 years ago

I would also like to know if this possibility is available.

Thanks!

brentp commented 4 years ago

hi, this seems pretty feasible. Does anyone have other metrics to include? I can track (in addition to median), max, min and percentiles.

lemetrec commented 4 years ago

Hey Brent,

Thanks for the response. I mean yes I think a couple of metrics like this can always interest depending on projects/specific biologies... Especially Min and Max, maybe also SD or CoV?

Thank you! Christophe

Biojenifer commented 4 years ago

Hi! It would be also great if you could include the mode too!

Thanks!

Z-Zen commented 3 years ago

I agree, I also would like to see this option available.

brentp commented 3 years ago

Hi, this is something that should be done with the d4 output and then the d4 utils or a simple python script.

brentp commented 3 years ago

see here: https://github.com/38/d4-format#run-stat-on-a-d4-file