Average depth/coverage before and after PCR duplicates cleanup

Question

[Begonia_pavonina]

Hello everyone,

I am using a pipeline (Paleomix) which mark duplicates in BAM files using Picard MarkDuplicates, but without removing them from the outputs.

I wish to compare the coverage in these files both with and without PCR duplicates filtering.

Would you know any tool or command adapted to this task?

I have tried to use different samtools depth scripts, but they all give me different results.

Thanks for your help!

[Arup Ghosh]

Try Mosdepth.

[Begonia_pavonina]

Thanks for the advice, Mosdepth looks a very interesting tool! Unfortunately, on the Github page I don't see the flag or any option for allowing/ignoring the PCR duplicates annotations in the BAM file. Would you remember the command used for it?

Answer 1

[ATpoint]

-F --flag <FLAG> exclude reads with any of the bits in FLAG set [default: 1796]

The duplicate flag is 1024, see http://broadinstitute.github.io/picard/explain-flags.html. I second the advice for mosdepth (unfortunately only available on Linux) because it is wickedly fast.

Edit 10.5.20: I managed to build mosdepth from source on Mac, see comment at the bottom of this issue: https://github.com/brentp/mosdepth/issues/103

[Begonia_pavonina]

That's very precious information as well ATpoint!

I did not make the relation between this flag and the annotations in the BAM file. Definitely going to use Mosdepth. Thanks!