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Subsample regions of too high coverage

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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...

  • #2
    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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    • #3
      @sbrohee

      Thank you for the suggestion. It works great!

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