I have GVCF files generated from deepvariant and I have a set of sites (in simplified vcf format) for which I want to extract genotypes for those sites. Is there an argument I can pass to GLNexus to genotype those vcf sites specifically?
Passing Intervals usually wont give the 0/0 genotypes I want to see if thats what the likelihoods indicate.
Otherwise my guess is I will have to go back to the bams. Thanks.
Greetings,
I have GVCF files generated from deepvariant and I have a set of sites (in simplified vcf format) for which I want to extract genotypes for those sites. Is there an argument I can pass to GLNexus to genotype those vcf sites specifically?
Passing Intervals usually wont give the 0/0 genotypes I want to see if thats what the likelihoods indicate.
Otherwise my guess is I will have to go back to the bams. Thanks.