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-   -   Subsample regions of too high coverage (http://seqanswers.com/forums/showthread.php?t=82781)

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 (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 01-27-2020 02:13 AM

@sbrohee

Thank you for the suggestion. It works great!


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