Hi, when using VariantRecalibrator, there is a mode option (--mode) for the choice of SNP and indels. I noticed in the Best Practice, the recalibration of SNPs and indels are discussed separately, so I was just wondering when running VariantRecalibrator, can I supply "-resource" option both indel and snp resources, and then get the two types of variants recalibrated at the same time ? or shall I do SNP and indels separately, and -resource is just one variant type?
Thanks!
Thanks!