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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

LeftAlignIndels not recognizing input/reference/output strings

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    Gökalp Çelik

    Hi Amy Reese

    Are you running GATK4 from the gatk script? Looks like parameter interpretation is lacking here. Possibly your python version could also be causing issues as well. Can you make sure that gatk script uses python3 version >= 3.6 ?

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    Amy Reese

    Hi Gokalp Celik,

    Yes, GATK4 ("Using GATK jar /home/areese/.conda/envs/WES_dev2/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar") and my "WES_dev2" conda env uses python 3.11.7 (see below).

    (WES_dev2) [Thu Mar 14 02:24 PM] areese /home/shared/repos/RNA-seq_develop 
    $ which python && python --version
    ~/.conda/envs/WES_dev2/bin/python
    Python 3.11.7

    Amy

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    Gökalp Çelik

    Hi again. 

    I tried reproducing the error that you are facing and the only time I could reproduce this error is when variables are not set properly. 

    Can you try running the tool without using variables for file paths? If the tool runs properly then it is definitely an issue with your exports. 

     

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    Amy Reese

    I did try that, but I'll start over and re-create the bams and the variables in case there was something that I missed along the way, and try again. I'll comment here if it still doesn't work for me after the restart. Thank you for your help.

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