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06-07-2018, 06:33 AM
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#1 |
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Member
Location: Brussels, Belgium Join Date: Sep 2011
Posts: 21
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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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06-08-2018, 02:12 AM
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#2 |
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Member
Location: Brussels, Belgium Join Date: Sep 2011
Posts: 21
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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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01-27-2020, 02:13 AM
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#3 |
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Junior Member
Location: RU Join Date: Oct 2011
Posts: 8
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@sbrohee
Thank you for the suggestion. It works great! |
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| Tags |
| bam, coverage, samtools, subsampling |
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