Entering edit mode
7.4 years ago
aylward.megan
▴
10
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.
