Currently the "Log in with Google" button redirects you to a "Page not found." This is an issue that our forum vendors are working on fixing. In the meantime, while on the "Page not found" you can edit the URL to delete the second gatk, firecloud, or wdl (depending on what subforum you are acessing).
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