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.
I didn't think it would be helpful to have the user have to explicitly specify USE_VCF_INDEX=true if they pass an intervals file.  I added an explicit check for the index if they are using the intervals file a bit further down in the code now.