If genotype data is available for the same individuals, at what stage would the data be most useful?
Should it be added at calling or VQSR (Variant Quality Score Recalibration) stage as a set of known variants with known genotypes?
Or rather use it afterwards to assess genotype concordance?
Should it be added at calling or VQSR (Variant Quality Score Recalibration) stage as a set of known variants with known genotypes?
Or rather use it afterwards to assess genotype concordance?