Laura Gauthier
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Activity overview
Latest activity by Laura Gauthier-
Laura Gauthier commented,
So happy to hear you were successful! We've solved a surprising number of issues over the years by throwing away poorly behaved LCR regions. Always a good tool to have in one's back pocket.
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Laura Gauthier commented,
OMG it's the QUAL! Your stack trace leads me to https://github.com/broadinstitute/gatk/blob/ebd8a275bea63b34e55f29e89a0a34aea78cce43/src/main/java/org/broadinstitute/hellbender/tools/walkers/gnarl...
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Laura Gauthier commented,
Hi Ryan Collins! The secondary issue you're seeing with the JNI issue might be because of the GenomicsDB version mismatch. Can you try running the SelectVariants as a workflow with the 4.6.1.0 vers...
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Laura Gauthier commented,
Well that's disappointing, but thanks for reporting back.
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Laura Gauthier commented,
Hi Matt! The GATK devs are not Cromwell superusers, but you could try the Cromwell-specific slack workspace: https://join.slack.com/t/cromwellhq/shared_invite/zt-2r05hmi3 If no one there is able to...
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Laura Gauthier commented,
Hi Phoebe We've done this in the past in the form of exomes plus ~20X whole genomes and it worked pretty well. Most of our annotations for filtering are built so that they compare the distribution...
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Laura Gauthier commented,
Isadora Machado Ghilardi that's a google cloud path. You can access files like that with the `gcloud` utilities or, since that one's public, though the google cloud console: https://storage.google...
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Laura Gauthier commented,
Hi yx zhang, That error would certainly stop VariantAnnotator from completing. Are you running the latest GATK (4.5.0.0)? I remember fixing a very similar htsjdk exception to provide more informa...
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Laura Gauthier commented,
Hi yx zhang, Looking at the code, the AF used in the PossibleDeNovo annotation is derived from the genotypes in the VCF: https://github.com/broadinstitute/gatk/blob/264040448aa8b8a580f7f818731c80dc...
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Laura Gauthier commented,
Hi Allan Daly, This is not unexpected. There's some (perhaps undocumented) random behavior of the QD annotation that applies here: https://github.com/broadinstitute/gatk/blob/cfd4d87ec29ac45a68f13...