Alijah O'Connor
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Recent activity by Alijah O'Connor Sort by recent activity-
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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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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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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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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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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Some MarkDuplicates chunks take a very long time to run
This run was done using GATK 4.1.6.0, the input BAM had ~600M reads. I'm curious why some chunks of MarkDuplicates take so long to process. Most of the chunks take 2-4s, while others can take up ...
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GATK4 Best Practices -- SetNmMdAndUqTags
In some places, I'm seeing that running SetNmMdAndUqTags before BQSR is not part of the GATK best practices, but in other places (including the GATK GitHub page) this tool is included. I'm just cu...
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BQSR --use-original-qualities
When looking at the GATK processing for variant discovery WDL script, I noticed that the Broad team use the parameter --use-original-qualities in both of the BQSR steps. Why is this the case? Wou...
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(GATK v4.1.6.0) Mutect2 bamout reports fewer reads than VCF AD
I've read many posts regarding differences in VCF allele depth and original (and bamout) allele depths; however, these discussions seem to be mostly about the read filtering that Mutect performs in...
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(GATK v4.1.6.0) Mutect2: More than two reads with same name found warning
11:34:20.535 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment. I've been following the discussions for this warning (and at one-time e...