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Old 06-07-2018, 07:33 AM   #1
Location: Brussels, Belgium

Join Date: Sep 2011
Posts: 21
Default 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 is offline   Reply With Quote
Old 06-08-2018, 03:12 AM   #2
Location: Brussels, Belgium

Join Date: Sep 2011
Posts: 21

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.
sbrohee is offline   Reply With Quote
Old 01-27-2020, 03:13 AM   #3
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Location: RU

Join Date: Oct 2011
Posts: 8


Thank you for the suggestion. It works great!
nazen is offline   Reply With Quote

bam, coverage, samtools, subsampling

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