Other

Base Recalibrator " No Positional Argument is defined for this tool"
- megha thippanna
- January 27, 2023 05:40
0 votes 0 comments
ApplyVQSR: "[W::bgzf_read_block] EOF marker is absent" and "[tabix] the index file exists." errors
- Bob Ye
- January 25, 2023 23:12
0 votes 0 comments
Liftover Picard hg19 to hg38: variants were not successfully lifted over
- Andres Caballero
- December 09, 2022 18:39
2 votes 2 comments
gatk4-GenotypeGVCFs.nf doens't recognize Primary_000001F chromosomes for process GatherVcfs
- Carole Couture
- December 08, 2022 15:19
0 votes 0 comments
HaplotypeCaller confuses introns as long deletions
- Vladimir Souza
- November 09, 2022 23:03
- Edited
0 votes 3 comments
error when running ASEReadCounter
- behzad
- October 27, 2022 11:20
0 votes 2 comments
SortSam - Question about I/O error
- Henry
- October 27, 2022 08:20
0 votes 2 comments
Does GATK4 BaseRecalibrator not understand relative paths?
- Eva (Evander)
- October 17, 2022 12:51
0 votes 10 comments
CombineGVCFs - possible to restart/continue run?
- medgen
- October 11, 2022 14:01
0 votes 5 comments
CGA3_WES_Characterization_Pipeline_v0.2_Jun2019 PoN Errors...
- Rose Gold
- September 28, 2022 14:32
0 votes 1 comment
GenomeSTRiP SVPreprocess error
- Jibin Jeong
- September 15, 2022 04:51
- Edited
1 vote 1 comment
Genomestrip: Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing
- Senwei
- April 27, 2022 07:59
1 vote 2 comments
Cromwell metadata of huge workflows
- Rafal Gumienny
- April 07, 2022 12:24
- Edited
0 votes 1 comment
Genomestrip preprocessing error
- chae chae
- March 08, 2022 03:41
- Edited
0 votes 13 comments
change the memory when running SVPreprocess
- zzq
- January 11, 2022 06:21
- Edited
0 votes 2 comments
VariantsToTable positional argument eror
- Owen Hudson
- December 14, 2021 17:22
0 votes 1 comment
Dictionary cannot have size zero error
- Nish314
- November 20, 2021 00:20
- Edited
0 votes 1 comment
CNNScoreVariants carshes with java.lang.NullPointerException with Python 3.8 & JDK 1.8
- KUMAR Chandan * TCS
- November 02, 2021 09:56
0 votes 1 comment
CalculateContamination 4.1.2.0 org.apache.commons.math3.exception.TooManyEvaluationsException
- 陈星瀚
- October 29, 2021 09:21
0 votes 1 comment
HaplotypeCaller inconsistency with different interval lists
- Gytis Mackevičius
- September 10, 2021 05:53
- Edited
0 votes 5 comments
My recalibration table from BaseRecalibrator is empty
- Calum Tattersfield
- August 25, 2021 18:14
- Edited
0 votes 5 comments
SplitNCigarReads does not seem to split reads properly as it was before 3.8-1?
- SkyWarrior
- June 21, 2021 13:29
- Edited
0 votes 7 comments
Running Genome STRiP SVPreprocess, but I got error message: "Invalid command line: Malformed walker argument: Could not find walker with name: ComputeInsertSizeHistogramsWalker"
- Norio Tanaka
- June 15, 2021 14:22
0 votes 4 comments
GenomicsDBImport - A USER ERROR has occurred: Failed to create reader from file: 2.0
- Jared Johnson
- May 07, 2021 20:44
0 votes 1 comment
sample_gender.report.txt is empty when running SVpreprocess restricted to chromosomes
- zzq
- April 16, 2021 11:52
- Edited
0 votes 8 comments
How do I keep a glob from copying a file in Cromwell / WDL
- Gregory Dougherty
- March 09, 2021 00:24
0 votes 1 comment
How to Fix the follow ValidateSamFile error ?
- Luis Enrique Romero Cruz
- March 06, 2021 03:51
0 votes 1 comment
BaseRecalibrator on MT .bam files
- Sharon Cox
- February 19, 2021 09:48
- Edited
0 votes 1 comment
LiftoverVcf: hg19 to hg38 all variants mismatched
- Ken Hanscombe
- February 17, 2021 14:13
0 votes 3 comments
Error when trying to generate the second recalibration table for AnalyzeCovariates
- ISmolicz
- February 17, 2021 12:03
0 votes 10 comments

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GATK Team Out of Office

The GATK team will be out of office during December 9th 2022 to January 9th 2022 in observance of the holidays. We will not be able to answer posts from within this period. If you are still experiencing issues when we are back, please re-post your inquiry.