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. Have the code to use a customCommandLineValidation to check that the VCF files have index files if the user sets the USE_VCF_INDEX parameter or if the user passes intervals to the tool.
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.
Have the code to use a customCommandLineValidation to check that the VCF files have index files if the user sets the USE_VCF_INDEX parameter or if the user passes intervals to the tool.

broadinstitute/picard,annkupi/picard,broadinstitute/picard,alecw/picard,nh13/picard,broadinstitute/picard,nh13/picard,alecw/picard,broadinstitute/picard,broadinstitute/picard,annkupi/picard,alecw/picard,alecw/picard,annkupi/picard,nh13/picard,nh13/picard,annkupi/picard