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CombineGVCFs generate idx files way bigger that HaplotypeCaller

I used HaplotypeCaller in GVCF mode. The output g.vcf files came out with g.vcf.idx files. On the next step, I am using CombineGVCFs on the g.vcf files. The tool is regenerating the g.vcf.idx files. This is example warn message:
WARN 12:45:50,628 RMDTrackBuilder - Index file /path/to/sample1.g.vcf.idx is out of date (index older than input file), deleting and updating the index file.
My biggest worry is that the new idx file is way much bigger (the original was 166472 bytes and the new is 217546623 bytes! Is this ok?


Issue · Github
by Sheila

Issue Number
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Best Answer


  • SheilaSheila Broad InstituteMember, Broadie admin


    Hmm. I have not heard of this before. Is the larger index file for the combined GVCF or for the original input single sample GVCF?


  • drtamermansourdrtamermansour USAMember

    for the original input single sample GVCF

  • SheilaSheila Broad InstituteMember, Broadie admin


    I need to check with the team and get back to you.


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