I was trying to extract genotype for every sample, including sites where the MAF doesn't pass the minimal threshold, by setting output_mode EMIT_ALL_CONFIDENT_SITES. Especially, I am curious about the genotype likelihood for each of the potential genotypes.
However the result in VCF shows GT:AD:DP:GQ:PL information for variant sites, and shows only GT:DP in Homo-ref sites, is there a way to get the genotype likelihood for homo-ref sites?
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Why the format field is different between variant sites and homo-ref sites?
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