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

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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...
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Old 06-08-2018, 02:12 AM   #2
sbrohee
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OK... I just ran into a great tool that seems to do exactly what I wanted. It is called VariantBam (https://github.com/walaj/VariantBam, https://www.ncbi.nlm.nih.gov/pubmed/27153727).

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

I hope it will be useful for some of you.
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