Hey, has anyone worked with two steps of VQSR (i.e. the successive application of VariantRecalibrator and ApplyRecalibration) for the non-human genomes?
You know, the human genome data have good truth and known resource datasets (HapMap , Omni , 1000G, dbSNP) which are already available for VQSR analysis. However, I do not have idea how to do it with mouse genome because I need to generate my own resource set. Anyone has experiences on this?
I did HARD SNP variant filtering using VariantFiltration of GATK since my variant file was produced by UnifiedGenotyper. Is VQSR unnecessary and I can skip this step since it looks a little challenge to me?