myourshaw
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Activity overview
Latest activity by myourshaw-
myourshaw commented,
After further investigation, it appears that the problem may have been introduced between GATH 4.2.1.0 and 4.2.2.0, contrary to our original suspicion that it was introduced in 4.1.3.0. After gathe...
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myourshaw created a post,
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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myourshaw created a post,
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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myourshaw commented,
This problem appears to be a bug in the version of Picard that is contained in GATK 4.2.0.0. When will GATK be updated with this fix? "This bug has been fixed in Picard release https://github.com/b...
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myourshaw commented,
Additional information. I tried to demultiplex the same data with IlluminaBaseCallsToFastq, which had the same falure to demultiplex. All reads were in the UNKNOWN fastq files. No reads were in any...
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myourshaw commented,
My guess is that the problem starts with IlluminaBaseCallsToSam. And the problem is with matching the barcodes in the BASECALS_DIR/BARCODES_DIR with those in the LibraryParams.
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myourshaw created a post,
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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myourshaw created a post,
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...