Modify GenotypeConcordance to explicitly require that the VCF files be indexed if an interval file is specified

Modify GenotypeConcordance to explicitly require that the VCF files be indexed if an interval file is specified.  Otherwise it would blow up, somewhat more obscurely, for lack of an index file.
We appear to be setting this to true silently. Do we want to require the user to specify UCE_VCF_INDEX=true if they also specify and INTERVALS file, and fail if they do not do so? Do we want to at least warn them?

Presumably the VCF reader will fail if a VCF index is not present. Should we test for this here, first, and provide a more informative failure message?