I was wondering if someone can suggest a way to detect loss of heterozygosity from the wes data. I've found a number of tools but they're mostly designed for tumor samples which is not my case. I have wes data of patients and am interested to see if we have haploinsufficiency of some known loci due to deletion of one copy of the gene.
I was thinking maybe first detecting ROH and if they overlap with my loci, then checking for coverage around that region. But I'm not sure if when we have only one copy of the gene, it would definitely alter the coverage in wes.
Thanks in advance!