Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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