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Downsampling by coverage

Hi the team,

Maybe this is a stupid simple question, however, but after I reading the introduction document in our forum here and also check the GATK source code, I didn't figure out it, so, thank you for your help.

Say, I set downsampling by coverage for a GATK tool, like RTC, for those region (let's assume that we are analyzing small target sequencing data) on which the total number of reads is less than the coverage we set for downsampling, what will GATK do? Just leave those region alone?


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