Subsample regions of too high coverage

[sbrohee]

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]

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.

[nazen]

@sbrohee

Thank you for the suggestion. It works great!