The front line support team will be unavailable to answer questions until May 27th 2019 as we are celebrating Memorial Day. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
I want to look for the compound heterozygous in a trio. For the same I have already called the variants through Haplotye caller and then applied hard filters (as the sample size was very low 7 exomes). Now if we want to look for compound heterozygous in the family I should be using Phase by Transmission (Genotype refinement). I am not sure where I can find the --supporting file i.e., ALL.phase3.20130502.biallelic_snps.integrated.sites.vcf as suggested in the Genotype refinement link https://www.broadinstitute.org/gatk/guide/tagged?tag=genotyperefinement. Any suggestion would be appreciated