Other

How to run muTect without normal sample? Answered
- Yingjie Zhu
- July 11, 2022 21:35
1 vote 3 comments
Accessing the resource bundle. Answered
- nagam surya
- June 28, 2022 18:35
0 votes 6 comments
markDuplicatesSpark running out of memory Answered
- Matt Snyder
- June 09, 2022 19:34
0 votes 3 comments
Hard filters on VariantFiltration following HaplotypeCaller; Filter contains an illegal character Answered
- Graeme Thorn
- May 27, 2022 21:05
- Edited
0 votes 5 comments
Genomestrip: Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing
- Senwei
- April 27, 2022 07:59
1 vote 2 comments
Refseq accession number and version number in Funcotator Answered
- TMB
- April 26, 2022 04:13
0 votes 4 comments
CNNScoreVariants Issues with environment and Java version Answered
- Kathrin B
- April 13, 2022 15:07
- Edited
0 votes 6 comments
Fontconfig error in the newest gatk docker image Answered
- SkyWarrior
- April 10, 2022 09:02
- Edited
0 votes 1 comment
Cromwell metadata of huge workflows
- Rafal Gumienny
- April 07, 2022 12:24
- Edited
0 votes 1 comment
vulnerability issue for gatk-package-4.2.5.0-local.jar Answered
- John Yu
- March 09, 2022 14:27
0 votes 4 comments
Local WDL Mitochondria Pipeline - Import failed Answered
- Michael
- March 08, 2022 09:25
- Edited
0 votes 1 comment
Genomestrip preprocessing error
- chae chae
- March 08, 2022 03:41
- Edited
0 votes 13 comments
Error in GenomicsDBImport: Invalid deflate block found Answered
- Lauren Hennelly
- February 26, 2022 20:26
1 vote 6 comments
GC overhead limit exceeded using Mutect2 only tumor version Answered
- Shirliya Dadon
- February 09, 2022 12:53
- Edited
0 votes 5 comments
GATK R plots with R v4.1.2 Answered
- Franz Gassner
- January 24, 2022 09:36
0 votes 3 comments
change the memory when running SVPreprocess
- zzq
- January 11, 2022 06:21
- Edited
0 votes 2 comments
Error in running GenomicsDBConfigException Answered
- Shivangi Agarwal
- December 20, 2021 14:51
0 votes 12 comments
VariantsToTable positional argument eror
- Owen Hudson
- December 14, 2021 17:22
0 votes 1 comment
CollectRnaSeqMetrics GL000220 test not counting ribosomal reads Answered
- rcorbett
- December 06, 2021 18:45
0 votes 5 comments
MarkduplicatesSpark failed Answered
- lid.zigh
- November 23, 2021 13:44
0 votes 5 comments
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
Contamination calculation on single file don't detect contaminated samples Answered
- Vladislav Maximov
- October 14, 2021 15:03
0 votes 7 comments
GenomincsDBImport Failed to create reader from file: An index is required, but none found., for input source: Answered
- Morgan Sparks
- October 12, 2021 11:46
0 votes 6 comments
markduplicatesSpark .bam.parts output error (directory already exists) Answered
- Morgan Sparks
- September 30, 2021 16:31
0 votes 3 comments
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
Funcotator gnomAD MAF columns Answered
- TMB
- August 23, 2021 02:04
0 votes 2 comments
Can't explain the number of reads FilterSamReads outputs Answered
- Aki Jarl Laruson
- July 28, 2021 23:29
0 votes 8 comments

Welcome

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.