How to restore an interrupted execution while running HaplotypeCaller

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David Medina

• December 03, 2022 13:46

Hi, everyone

Recently I was running  a process with HaplotypeCaller that was taking couple of days but the process stopped running at region chr6:114178160. I wonder if it is possible to restore the HaplotypeCaller running session from this specific region. Do I have to run the entire process again?

Additional available information:
a) GATK version used: v4.1.9.0
b) Exact command used:

command="$gatk HaplotypeCaller -R $ref -ERC GVCF -O $gvcf" #-L $intervals"
for i in "${bams[@]}"; do
    command="$command -I $i"
done

# run GVCF
eval "$command"

Thank you

0

• 

  Anthony DiCi

  • December 05, 2022 15:23

  Thank you for your post, David Medina ! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

  Please see our Support Policy for more details about how we prioritize responding to questions. 

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