Genotype refinement with incomplete "trios"
I am doing a WGS project on a family with seven siblings. We have data on the mother but the father passed many years ago. I tried splitting variant recalibrated vcf file and ped file into "trios" with just the mother and a sibling (seven times) then running PhaseByTransmission on the combined vcf. The job was successfully completed but nothing appears phased (all "/," and no "|") in the output vcf.
I also tried the variant recalibrated vcf file separately with ReadBackedPhasing. The job was successfully completed as well but again nothing appears phased (all "/" and no "|" or assigned "PQ" scores).
The ProduceBeagleInput walker (to use Beagle for genotype refinement) appears to only support unrelated individuals and my set involves related individuals. Do you have any other suggestions for phasing incomplete "trios?"
Thanks in advance!