Robert Bremel
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Funcotator Problem docker image code:400 message: Bucket is a requester pays bucket but no user project provided.
REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: It has been down with this problem all week. It had the same problem in February and was fi...
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FuncotatorDataSourceDownloader problem at google
Had a problem with Funcotator yesterday thought maybe the datasources had been corrupted so tried to download new set. Got same error docker version 4.6.1.0 = docker "latest" code: 400mes...
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Funcotator Problem docker image code:400
Have been using this syntax for 4-5 yrs. Worked a week ago? (gatk) root@927aafec98f5:/gatk# ./gatk Funcotator --versionUsing GATK jar /gatk/gatk-package-4.4.0.0-local.jarRunning: java -Dsamj...
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Funcotator problem
I started two Docker containers of Funcotator this morning and they both crashed in about the same place. I had started them earlier but they seemed to have finished quicker than they should have...
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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...