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Re-starting GenotypeGVCFs from certain position?


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.



  • SheilaSheila Broad InstituteMember, Broadie, Moderator


    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?


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