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alanhoyle

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Latest activity by alanhoyle
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    alanhoyle commented,

    The link above to see detailed explanations appears to redirect back to this page here and in other versions of this page.   Rather than the looping "zendesk" links, perhaps it should go to this UR...

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    alanhoyle commented,

    This pull request has been accepted in Picard, so I suspect it'll propagate forward to GATK eventually.  

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    alanhoyle commented,

    I've made a pull request that could address this.  https://github.com/broadinstitute/picard/pull/1671

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    alanhoyle created a post,

    RExecutor/ProcessExecutor invalid file argument error

    In Picard's RExecutor process, % symbols in the requested output filename cause the R process to crash with a "invalid 'file' argument" generated by R's pdf() function.  The work-around here is to ...

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    alanhoyle commented,

    I've made a workflow that divides the regions using SplitIntervals --subdivision-mode BALANCING_WITHOUT_INTERVAL_SUBDIVISION and I think I have it working. I'm able to reconstruct the original inte...

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    alanhoyle created a post,

    Mutect2 parallelize input

    Can you please provide a) GATK version used 4.1.7.0b) Exact GATK commands (question about options)c) The entire error log (n/a) I've been running Mutect2 for a while now, currently 4.1.7.0.  Just t...

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    alanhoyle commented,

    One question I've seen repeatedly on several sites is about the difference between what exactly the bait and target intervals are supposed to represent.  It would be extremely useful if that explan...

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    alanhoyle commented,

    Bhanu Gandham,  Am I correct that the OxoG and FFPE filtering has been removed from Mutect2/GATK?   I'm looking at the mutect2_wdl documentation, and it lists "Mutect2_Multi.artifact_modes" and "Mu...

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    alanhoyle commented,

    Thanks Bhanu Gandham.   By digging into the WDL, it appears that the orientation bias filter is available at the GATK command line too.  Here is line 597 in the WDL:   ~{true='--f1r2-tar-gz f1r2.t...

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    alanhoyle commented,

    Bhanu Gandham, that doesn't answer the underlying question though:  Has the functionality of FilterByOrientationBias been reimplemented somewhere else in the GATK?  If so, how does one use it?