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Alijah O'Connor

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  • Interpretting CrosscheckFingerprints metrics

    1. Community
    2. Somatic

    For my somatic-caller workflow, I am exploring using the CrosscheckFingerprints tool to determine if either sample of a tumor-normal paired group has been swapped (i.e. the fastqs are not actually ...

    • Alijah O'Connor
    • 6 followers
    • 12 comments
    • 0 votes

  • Optimizing Mutect2 threads with a scatter-gathering approach

    1. Community
    2. General Discussion

    Getting deeper into a custom-implementation to scatter-gather multiprocessing with Mutect2, I noticed (via htop) there were 15 child processes associated with each actual Mutect2 call.  Although mo...

    • Alijah O'Connor
    • Edited
    • 4 followers
    • 3 comments
    • 0 votes

  • Scatter Count recommendations

    1. Community
    2. Somatic

    I'm looking into parallelizing my somatic whole-exome pipeline using the scatter strategy (though recreating it using Bash and Python).  That said, I've been looking through the wdl scripts on the ...

    • Alijah O'Connor
    • Edited
    • 2 followers
    • 1 comment
    • 0 votes