Laura Gauthier
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Activity overview
Latest activity by Laura Gauthier-
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...
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Laura Gauthier commented,
Hi Wei-Yang BAI, There is no DRAGEN mode for joint calling -- it's only single-sample VCF or GVCF. You can run our best practices for joint calling on DRAGEN GVCFs for most DRAGEN versions, but a f...
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Laura Gauthier commented,
HaplotypeCaller won't do multi-sample GVCFs and you're going to run into issues combining multiple multi-sample genotyped VCFs. Most importantly, you won't have reference information to get confid...
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Laura Gauthier commented,
Just following the GATK Best Practices does not mean that your pipeline is validated. Typically validation refers to a specific truth comparison that you can define yourself. For our clinical sequ...
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Laura Gauthier commented,
Hi Goran Rakocevic, Unfortunately with the low-pass WGS study design, you're going to be limited to common variants, but on the other hand seeing a variant in multiple samples is pretty good eviden...
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Laura Gauthier commented,
Hi Dahn-young Dong, No-call doesn't really have a strict definition, but I would agree that anything with no depth is worth excluding. I'd recommend you trust DP over genotype call. To calculate s...