Is there a standard way to check sequencing quality from a VCF? For example, if you're working on a case/control exome project and you are supplied with VCFs for each sample, but don't have access to BAMs or FASTAs, how would you go about checking that the supplied VCFs are good enough to be included in the study?
Some common metrics I have seen are Ti/Tv, concordance with dbSNP, proportion of missense, synonymous variants, etc. Is there anything else one could check? Are there any tools that will do these calculations for you?