The frontline support team will be unavailable to answer questions until May27th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
VariantRecalibrator and CalculateGenotypePosteriors requires the same 1000G vcf file?
I am using the best practice pipeline to call genotypes from whole-genome sequencing data on 67 human samples. In the examples on the website, VariantRecalibrator uses 1000G_phase1.snps.high_confidence.hg19.sites.vcf as one of the training examples. However, CalculateGenotypePosteriors uses 1000G_phase3_v4_20130502.sites.vcf as the supporting file. Is this intentional? Does it matter which version of 1000G vcf is supplied to CalculateGenotypePosteriors?