Hello! I need a step to step Guide on how to Create a Truth and Training set for VariantRecalibrator GATK v4.1.4. The Guide available on GATK website was not helpful enough and I have yet to make progress.
I have downloaded a list of known indels BQSR file from 1000bullgenome website and plan to use it for the -resource part of the command line. Kindly mention the steps necessary to turn this file into a suitable resource file for variant recalibrator step of GATK.