According to GATK best practice, it is recommended that different VQSR models be built for SNPs and INDELs, because the annotations for high-quality SNPs and INDELs are systematically different (if I understand it correctly). Since annotations for good variants on autosomes could be different from those on X chromosome, e.g., DP for good variants on X chromosome could be substantially smaller than DP on autosomes due to having large number of male samples, it seems reasonable to build VQSR models separately for X chromosome and autosomes. However, no such advice is proposed on GATK website.
My question is:
Should we build VQSR models separately for autosomes and X chromosome? If yes, we will have 4 VQSR models: Auto SNPs, Auto INDELs, X SNPs and X INDELs.