c) Why do I see only one sample in my combinedGVCF? I ran Haplotype caller on 250 individual samples under -ERC GVCF (separately for each individual). Then merged them using CombineGVCF and ran the GenotypeGVCFs.
My final VCF is recognized as just ONE sample. Is there a way to merge gvcfs without losing the number of individuals? I can't perform any population genetic analysis with just 1 sample.
Please sign in to leave a comment.