@sbrohee
Thank you for the suggestion. It works great!
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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.Leave a comment:
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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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