Other

Invalid or corrupt jarfile error Answered
- Benjamin Singer
- November 30, 2022 00:55
- Edited
0 votes 2 comments
ShiftFasta creates empty intervals file Answered
- Ram
- October 21, 2022 07:56
- Edited
0 votes 4 comments
Error in Running command CreateExtendedIlluminaManifest Answered
- Nur Adlina Binti Mohd Affian
- October 03, 2022 09:21
0 votes 3 comments
Accessing the resource bundle. Answered
- nagam surya
- June 28, 2022 18:35
0 votes 6 comments
How can I build the GATK jar so that the intel native libraries are available? Answered
- Mark Schreiber
- September 22, 2022 16:49
0 votes 4 comments
libgkl_compression.so not found + Failed to detect Google Compute Engine in a GATK workflow Answered
- Marta Giovalli
- September 14, 2022 12:47
- Edited
0 votes 4 comments
How to run muTect without normal sample? Answered
- Yingjie Zhu
- July 11, 2022 21:35
1 vote 3 comments
VCF input example Answered
- Noam Rudberg
- August 07, 2022 09:45
0 votes 1 comment
GenomicsDBImport: Attempting to genotype more than 50 alleles Answered
- Nils Homer
- August 06, 2020 00:13
1 vote 9 comments
Cannot use haplotype caller on STAR-aligned data Answered
- David Condon
- August 05, 2022 15:49
0 votes 2 comments
MergeVcfs issue: Illegal character in fragment at index 1: ##fileformat=VCFv4.2 Answered
- Liyang Zhang
- August 03, 2022 08:02
- Edited
0 votes 1 comment
FindBadGenomicKmersSpark running indefinitely Answered
- Cher Wei Yuan
- August 02, 2022 02:25
0 votes 5 comments
Using the IndexFeatureFile, doesn't recognize -F flag Answered
- Gijs C
- July 30, 2022 12:21
0 votes 2 comments
GenomicsDBImport works in interactive shell, but not in a script Answered
- Guy Shapira
- July 21, 2022 22:05
0 votes 1 comment
Haploytpe caller shows me that 0 read(s) were filtered by: MappingQualityAvailableReadFilter etc. Answered
- pb
- July 13, 2022 14:15
0 votes 4 comments
MarkduplicatesSpark failed Answered
- lid.zigh
- November 23, 2021 13:44
0 votes 5 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
Refseq accession number and version number in Funcotator Answered
- TMB
- April 26, 2022 04:13
0 votes 4 comments
No results of CollectvariantCallingMetrics Answered
- Yenan
- November 30, 2020 07:13
0 votes 30 comments
CNNScoreVariants carshes with java.lang.NullPointerException Answered
- riederd
- January 17, 2020 15:29
1 vote 13 comments
CNNScoreVariants Issues with environment and Java version Answered
- Kathrin B
- April 13, 2022 15:07
- Edited
0 votes 6 comments
ApplyBQSR no positional argument is defined for this tool Answered
- Jose Aragon
- March 06, 2021 14:26
0 votes 7 comments
Fontconfig error in the newest gatk docker image Answered
- SkyWarrior
- April 10, 2022 09:02
- 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
Error in GenomicsDBImport: Invalid deflate block found Answered
- Lauren Hennelly
- February 26, 2022 20:26
1 vote 6 comments
Local WDL Mitochondria Pipeline - Import failed Answered
- Michael
- March 08, 2022 09:25
- Edited
0 votes 1 comment
Error in running SplitNCigarReads - htsjdk.samtools.util.RuntimeIOException Answered
- KATHIE NGO
- August 27, 2020 17:31
- Edited
0 votes 8 comments
GC overhead limit exceeded using Mutect2 only tumor version Answered
- Shirliya Dadon
- February 09, 2022 12:53
- Edited
0 votes 5 comments
Error in running GenomicsDBConfigException Answered
- Shivangi Agarwal
- December 20, 2021 14:51
0 votes 12 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.