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Print BAM file downsampled to coverage at given loci

zugzugzugzug Posts: 20Member


I'm trying to print a bam file downsampled to a certain coverage at given loci. What I've tried thus far is to use PrintReads with -dcov XXX, but as the documentation states, it will downsample to that coverage based on the beginning of the aligned read. Is there a way to get a bam file that has been downsampled to a (nearly) precise coverage at specified loci?

I am not using GATK to call variants or any other purpose, so I can't do it while calling variants.

Thanks for your help!

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