I'm looking for de novo mutations in children with Trisomy 21. I have sequence for 4 trios (mother, father, child with Trisomy 21). I have run Haplotype caller with ploidy 2 and with ploidy 3, then wrote a python script to make a new-gvcf (ploidy 2 for all but chromosome 21 and the ploidy 3 gvcf regions for chromosome 21). I'm about to run Gvcftovcf and I realize that also has a ploidy option. Since I'm running all individuals together in Gvcftovcf I'm not sure what to do about sample_ploidy option. The best I can come up with is to run with both ploidy options and combine via a python script (chromosome 21 ploidy 3 for the child, and the rest of the file as ploidy 2) as I did before.
Any other ideas?