Robert Bremel
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string length error generated by funcotator while processing a mutect2 vcf
A string length error is generated by functator while processing a vcf from mutect2. java.lang.StringIndexOutOfBoundsException: begin 1086, end 1089, length 1086 (more below) funcotator stops a...
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BuildBamIndex
REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: Have run this script many times previously but problem occurred with the 4.3.0 update After ...
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Funcotator missing cDNA, Codon, and Protein Change for some chromosomes
AnsweredI am using the :latest docker version of GATK, running on Docker Desktop on a high-end Windows 10 workstation with 128GB RAM I had a strange occurrence that seems to be a glitch in the system so...
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Mysterious Funcotator issue
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: Docker 4.2.0 b) Exact command used: ./gatk Funcotator -R mydata/refs/Homo_sapiens_assembly38.fasta -V mydata/PAAD_00034_...
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Funcotator and mutect2 coordinate system
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: b) Exact command used: c) Entire error log: If not an error, choose a category for your question(REQUIRED):a)How do I (....
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Can vcf file from mutect2 be used in RNAseq short variant discovery
AnsweredCan you please provide a) GATK version used b) Exact GATK commands used c) The entire error log if applicable. Docker gatk:latest The method suggested for RNAseq short variant discovery uses haplot...
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mutect2 vcf header
The final three lines in the mutect2 header above the column headers is listed as: ##source=Mutect2##tumor_sample=N31May2020##tumor_sample=T31May2020 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ...
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Funcotator Appears to have completed but with RunTimeException
Can you please provide a) GATK version used Docker 4.1.7.0b) Exact GATK commands used Funcotator -R mydata/refs/Homo_sapiens_assembly19.fasta -V mydata/P62820/analysis/P62820_mutect2_filtered.vcf ...
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How is tumor_f in Funcotator MAF
AnsweredCan you please provide a) GATK version used b) Exact GATK commands used c) The entire error log if applicable. Using most recent GATK docker. tumor_f is not one of the columns in the MAF specificat...
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Workaround for Missing Platform Identifier in BQSRPipelineSpark?
I have been running the GATK best practices workflow in Docker verion 4.1.7.0 and everything was working fine up to now. BQSRPipelineSpark complained about a missing platform specifier. It seems t...