
myourshaw
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Mutect2 unexpected false negative due to changes in smith-waterman parameters?
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.2.4.0b) Exact command used: "Mutect2 --f1r2-tar-gz AMOncoHS-A.f971840a-b541-4c77-baf0-1b990bbbace6.f1r2.tar.gz --tumor...
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unexpected variant calls by Mutect2 depending on ExtractIlluminaBarcodes --MAX_MISMATCHES
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: Picard 2.25.5, GATK 4.2.0.0b) Exact command used: c) Entire error log: If not an error, choose a category for your quest...
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IlluminaBasecallsToSam does not demultiplex NovaSeq barcoded reads
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.2.0.0b) Exact command used: gatk --java-options -Xmx26g \IlluminaBasecallsToSam \--BASECALLS_DIR /home/dnanexus/210323...
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Mutect2 false negatives
We have observed several situations where Mutect 2 has failed to report a known variant from a gene panel based on IDT probes. The latest example is JAK2 1849G>T Val617Phe GRCh38 chr9:5073770-50737...