SEQanswers (
-   Bioinformatics (
-   -   Subsample regions of too high coverage (

sbrohee 06-07-2018 06:33 AM

Subsample regions of too high coverage
Hi all,

Do you think there is an efficient way of downsampling only a few regions of a bam files (in my case the regions with a too high coverage).

The idea, would be too randomly remove reads in regions where the coverage is above a given coverage.

Indeed, in my analyses, those regions cause some steps of the pipeline to become really slow.

Thanks for all your suggestions...

sbrohee 06-08-2018 02:12 AM

OK... I just ran into a great tool that seems to do exactly what I wanted. It is called VariantBam (,

./variant highcoveragebam.bam -m maxcoverage -o reducedmaxcoveragebam.bam -b

I hope it will be useful for some of you.

nazen 01-27-2020 02:13 AM


Thank you for the suggestion. It works great!

All times are GMT -8. The time now is 08:32 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.