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GenotypeGVCFs very slow if index files from HaplotypeCaller are provided
I have a problem, that if I have index files for genomic VCF files generated by HaplotypeCaller when running GenotypGVCFs, the runtime increases dramatically - in a test example of 6 samples, from 2 minutes to 7 hours. The same version of GATK is used in both steps (3.3-0). Should I not be providing index files and let GenotypeGVCFs always generate them on the fly? It adds time as sample number increases. Attached are log files from both runs.