Alijah O'Connor
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Activity overview
Latest activity by Alijah O'Connor-
Alijah O'Connor created a post,
Mutect --genotype-germline-sites status
If not an error, choose a category for your question(REQUIRED):e) Will Mutect2's --genotype-germline-sites be in future releases? I notice that this flag is still set to `EXPERIMENTAL` in the Mutec...
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Alijah O'Connor created a post,
Bamout haplotypes are much worse than bamout tumor reads would suggest
Background: I was triaging a particular passing variant call from Mutect2 (there was no evidence for this variant in the original BAMs), so I ran Mutect2 again producing the bamout. Top panel =...
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Alijah O'Connor commented,
I haven't found any information about f1r2-min-bq, but here is GATK issue that goes into the min-base-quality-score parameter a bit (https://github.com/broadinstitute/gatk/issues/6045)
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Alijah O'Connor created a post,
Clarity on Variant Callers being "optimized for UMI-containing data"
If not an error, choose a category for your question(REQUIRED):b) What does (......) mean? I was reading https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mute...
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Alijah O'Connor commented,
Thank you! Yes, this very helpful in understanding exactly what behavior to expect when I'm using this parameter.
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Alijah O'Connor commented,
For sure, but I'm more trying to get at the exact operations that are going on under the hood. The documentation doesn't really help with the questions I posed in the original post. An additional ...
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Alijah O'Connor created a post,
Interval Filtering -- How does it actually work?
This is a general question about the inner-working of interval filtration (i.e. --intervals, -L parameters with a supplied "intervals"-containing file). Since this functionality is provided for a ...
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Alijah O'Connor commented,
This appears to be a python problem: Tool returned (STDOUT): -42 (which is the value I set for EXIT_CODE_WHEN_MISMATCH) Python exit code (via subprocess.call()): 4
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Alijah O'Connor created a post,
CrosscheckFingerprints EXIT_CODE_WHEN_MISMATCH doesn't seem to work
I am trying to test my GATK python-based wrapper module, and I have call to CrosscheckFingerprints that should be in the NO-VALID-CHECKS situation (i.e. should raise the exit code passed into the E...
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Alijah O'Connor commented,
Thanks for clarifying some of this Bhanu Gandham, though I would like to mention that compared to many of the other GATK tools, I find the documentation of this tool to be quite confusing. I'm not ...