Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!
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?