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Percent progress in HaplotypeCaller GATK 4

RafaelMarcondesRafaelMarcondes Louisiana State UniversityMember

Hi all
In GATK 3, HaplotypeCaller printed out a % progress and estimated time to finish. GATK 4 doesn't seem to do that anymore, is that correct? Or is there an option I can activate to do it? And if not, can anyone suggest a workaround for me to get an idea of how long this thing is going to take to finish? Thanks!


  • manolismanolis Member ✭✭✭
    edited January 7

    Hi, in my case I run in a local linux server and I use a very simply bash command, "date"

    echo -n "START: "; date
    echo -n "END: "; date

    For a WGS, using a specific host and setting, I have always the same run time, considering always the same design and a similar coverage (30-40X), for example:

    START: Wed Jan 1 22:13:22 CET 2020
    END: Sat Jan 4 18:39:39 CET 2020

    around 3 days

    Moreover in the log files you can see when start and end you run ...

    22:13:27.564 INFO HaplotypeCaller - ------------------------------------------------------------
    18:39:39.205 INFO ValidateVariants - Shutting down engine


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