To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

Re-starting GenotypeGVCFs from certain position?

Hi,

I was joint genotyping about 400 samples with GenotypeGVCFs when I had node failure. The run was at about 83% which two weeks to get there. Is there a way for me to continue from this position rather than re-start the entire joint genotyping process? Thanks.

Tagged:

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @mmargres
    Hi,

    Unfortunately, you will have to re-start your run. There is no way to ensure you will get correct results without restarting. Perhaps you can try running per-chromosome then merging the VCFs, so these failures will not affect you so much?

    -Sheila

Sign In or Register to comment.