What to do with really high coverage samples for variant calling?
I have data from amplicon sequencing that is extremely high depth (average of 148K reads at my variants of interest). In running haplotype caller with a single sample and groups of samples, I noticed that I am getting drastically different genotyping calls depending on the run. The outputted allele depth seems to be maxing out for most of samples between 100-500, I figured that is randomly sampling down to 250 reads and each time it producing different results because it is only sampling ~0.3% of my reads. After looking at the different forums and posts on this site I see now that apparently the dcov option doesn't work with haplotype caller and has been disabled. I've run my samples through unified genotyper and I could disable the downsampling and I am seeing the expected results. However, haplotype caller is more sensitive than unified genotyper so it is my understanding that haplotype caller should always be used. I also want to use haplotype caller because one of my variants is a small deletion. I am hoping you can advise me on how I might move forward. Should I just use unified genotyper or is there some change I can make in the haplotype caller to make it work? This is a very small region so I am not concerned about the increased computational time of it using all the reads to make a call.