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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

issue with gatk4-exome-analysis-pipeline when running given sample data

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6 comments

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    Jason Cerrato

    Hi Umang,

    Happy to see if I can help here. Am I correct in understanding that you are running this on a personal Cromwell?

    Can you provide a link to the workflow you are using? Can you also provide the .log, stdout, and stderr files for your job?

    Many thanks,
    Jason

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    umang kumar

    Hi Jason ,

    It worked , we have made changes in UnmappedBamToAlignedBam.wdl   and BamProcessing.wdl  by adding "input_bam_index" variable and its file location 

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    Jason Cerrato

    Hi Umang,

    Glad to hear it worked!

    Kind regards,

    Jason

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    Aubrey Bailey

    I was able to reproduce this and have made a PR.

    https://github.com/gatk-workflows/gatk4-exome-analysis-pipeline/pull/18

    Thanks for the good reporting umang kumar !

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    Grace Miner

    Hi, I am having the same issue and getting the same error at the same step with the gatk4-genome-processing-pipeline.  I am new to running GATK workflows and don't understand how to implement your solution.  
    Where do you add "input_bam_index and the file location"? Any details regarding how you fixed the error would be greatly appreciated.  

    Best,

    Grace

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    umang kumar

    Hi Grace,

    GATK have made changes in there repository .Take the latest build .
    I got mail from them stating they identified the bug and made the changes.
    if not i mentioned the file name declare it in variable section.

    Regards
    Umang

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