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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.

Thank you,

Issue · Github
by Geraldine_VdAuwera

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