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Genotype likelihoods from HapMap SNPs
Hello the team,
My ultimate objective is to generate genotype likelihoods for SNPs throughout samples. I first used GATK to make a complete VCF file based the SNP variants in HapMap format, and then am going to employ the CalculateGenotypePosteriors module for that specific calculation. I indeed got a VCF file without any warning via calling "-V VariantsToVCF". However, the INFO field is empty (filled by zero's). I wonder how to supplement unbiased GL (and GP) to the VCF. It should be mentioned that I have no BAM file for the SNPs. thanks