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Lack of hard drive space in the middle of running GATK

TammyTammy Washington, DCMember

I ran out of hard drive space while combining a large number of GVCFs with the CombineGVCF Tool. I moved a bunch of files and have plenty of disc space now, but I'm wondering if my combined.g.vcf files will have errors... do I need to redo them? Is there some way to check for problems?


  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    I think bcftools can check the validity of gVCFs. GATK and vcftools can probably do the same. As a simple check you could make sure that the number of fields are identical for all records/lines. If I was in your shoes I would run the job again irrespective of all files passing all checks that I can think of.

  • TammyTammy Washington, DCMember

    I think I will redo the combined gVCF files even though they take quite a long time. It's not worth having errors from this. Thanks for the suggestions on checking the files!

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