alanhoyle
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Recent activity by alanhoyle Sort by recent activity-
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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This pull request has been accepted in Picard, so I suspect it'll propagate forward to GATK eventually.
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I've made a pull request that could address this. https://github.com/broadinstitute/picard/pull/1671
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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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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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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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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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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?
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A colleague noticed that there's now a ReadOrientationFilter in the Mutect Code . How does one use that? I don't see that mentioned in the command line for FilterMutectCalls or Mutect2. How does ...
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Is there any additional information about that? While I realize it was an "EXPERIMENTAL" tool, it would be nice to know why, and have some mention about that in the release notes. Has the functi...