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Genotype Refinement

anshikasanshikas MichiganMember

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


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