Entering edit mode
3.0 years ago
rthapa
▴
90
Hi, I am trying to optimize a genotyping protocol for a polyploid sample. I have pooled 100 individuals per sample and sequenced with novaseq. I want to know the optimum number of individuals and optimum depth for each sample. I am planning to subset different coverage like 10X, 20X etc from bam file to find the appropriate read depths comparing the allele frequency and heterozygosity across different depths. Do you have a any suggestion on how to determine the optimum number of individuals for pooling? Thanks
