User: a.j.wilson0000

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Johns Hopkins, Baltimore, USA
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1 year ago
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Posts by a.j.wilson0000

<prev • 5 results • page 1 of 1 • next >
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Having some ANNOVAR problems with mito variants.
... Several questions I'm hoping you guys can help me resolve: **1)** Does anyone know what build the current release of ClinVar uses for hg19? Is it UCSC hg19, or is it 1000 genomes GRCh37. I know it doesn't matter for autosomes, but I'm trying to import databases to ANNOVAR for mitochondrial variant ...
annovar clinvar written 9 weeks ago by a.j.wilson000010
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GATK's NuMT detection algorithm?
... Could anyone attempt to walk me through the logic of what is happening here? [Polymorphic NuMTs][1] > Number of alts indicates it could be an autosomal false positive. >**Overview:** >Potential polymorphic NuMT annotation compares the number of alts to the autosomal coverage Polymorphi ...
variant calling gatk mitochondria written 8 months ago by a.j.wilson000010 • updated 6 months ago by Biostar ♦♦ 20
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CollectHsMetrics per_base_coverage results quirk
... Hey all, I've recently been working with GATK's Mutect2 --mitochondria-mode for calling variants on chrM. I am testing the WDL Best Practices Pipeline on terra which employs a double alignment strat, along with a reverse engineered command line version for a single alignment strat. Recently tested ...
gatk mitochondrial variant calling written 11 months ago by a.j.wilson000010 • updated 10 months ago by houkto80
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Comment: C: GATK Terra Best Practices pipeline for Mito Variant Calling
... I'm fairly certain it's all been sorted on the lab side. We have new TWIST mito probes custom tailored to the rCRF that can pull out chrM piecemeal without disrupting the standard WES process. Auto filtering of amplified NuMTs is apparently done with FilterMutectCalls along with the default setting ...
written 12 months ago by a.j.wilson000010
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GATK Terra Best Practices pipeline for Mito Variant Calling
... Hey all. Currently working on a project to do mitochondrial variant calling on whole exome data. Our probes are about 120 bp and are setup to capture the entirety of the chrM contig at extremely high depth. We're currently looking at a few different tools, and the new GATK best practices MUTECT2 m ...
terra gatk wes variant calling written 12 months ago by a.j.wilson000010 • updated 10 months ago by houkto80

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