Question: Down-sample to one read per SNP loci per sample
gravatar for aylward.megan
3.6 years ago by
aylward.megan0 wrote:

Does anyone know if there is a way of downsampling to a coverage of 1x per sample at known SNP loci? I have tried GATK downsample but receive an error that the lower limit is 200x per SNP.

After aligning and SNP calling using a combination of high and low coverage samples I would like to take the called SNP loci and randomly sample one read per loci per sample.

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