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Philipp Hahnel

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Recent activity by Philipp Hahnel

  • Java Runtime Environment crash in FilterAlignmentArtifacts

    I am trying to run FilterAlignmentArtifacts on some Mutect2 output (after filtering etc), however, the Java Runtime Environment crashes. This is also the case for every other gatk docker version th...

    • 2 followers
    • 5 comments
    • 0 votes

  • scatter over optional array

    I have a case where I want to iterate over two arrays, one of which shall be optionally present or not. I created the test WDL below. In the case of create_inner_array = false it throws the error ...

    • Edited
    • 4 followers
    • 14 comments
    • 0 votes

  • file localization not working

    Hi, I've checked the other related articles on issues with file localization, and my problem doesn't seem to be amongst those. I've written a WDL to use samtools on a bam and a ref fasta.  1. Probl...

    • 3 followers
    • 18 comments
    • 0 votes