Other

ValidateSamFile behavior
- Robert Edgar
- February 17, 2020 18:07
1 vote 7 comments
Accessing the resource bundle. Answered
- nagam surya
- June 28, 2022 18:35
0 votes 6 comments
CNNScoreVariants Issues with environment and Java version Answered
- Kathrin B
- April 13, 2022 15:07
- Edited
0 votes 6 comments
Error in GenomicsDBImport: Invalid deflate block found Answered
- Lauren Hennelly
- February 26, 2022 20:26
1 vote 6 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
Truncated bam file after running ReplaceSamHeader(Picard) Answered
- kostas alexiou
- November 17, 2020 15:12
0 votes 6 comments
Dosages with Mutect2
- Leore Nehemie Bensabath
- July 24, 2020 08:36
0 votes 6 comments
RemoveNearbyIndels: CRSP
- Andrew Zhang
- May 13, 2020 06:49
0 votes 6 comments
How to set a COMPRESSION_LEVEL of ApplyBQSR
- Nickier
- April 26, 2020 10:34
0 votes 6 comments
jar for mutect 1.1.7
- Knight Ni
- April 19, 2020 17:08
1 vote 6 comments
User error: input files reference and features have incompatible contigs
- mons7re
- February 14, 2020 14:12
0 votes 6 comments
PathseqPipelineSpark stops without error message
- vitor heidrich
- February 07, 2020 00:44
0 votes 6 comments
options used during base recalibration
- janick mathys
- January 30, 2020 12:36
0 votes 6 comments
CombineGVCFs - possible to restart/continue run?
- medgen
- October 11, 2022 14:01
0 votes 5 comments
FindBadGenomicKmersSpark running indefinitely Answered
- Cher Wei Yuan
- August 02, 2022 02:25
0 votes 5 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
GC overhead limit exceeded using Mutect2 only tumor version Answered
- Shirliya Dadon
- February 09, 2022 12:53
- Edited
0 votes 5 comments
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
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
HaplotypeCaller - Shutting down engine - Encountering a large genome
- zyw
- December 07, 2020 02:27
0 votes 5 comments
SVDiscovery OutOfMemoryError.
- latte kim
- December 01, 2020 07:56
0 votes 5 comments
-DepthOfCoverage-ct not working in GATK 4.1.8.1
- Wei
- November 30, 2020 23:00
0 votes 5 comments
ReciprocalOverlapAnnotator error for Illumina data (both ERDS and CNVnator)
- Ghausia Begum
- June 04, 2020 04:22
0 votes 5 comments
Problem Installing and testing GATK-4.1.7.0
- Arjun Upadhaya
- May 04, 2020 06:34
1 vote 5 comments
GATK Runtime Error 3.8
- Nicholas Cho Rui Wen
- April 09, 2020 10:35
0 votes 5 comments
Dockerfile for genomes-in-the-cloud
- Tony Bendis
- March 10, 2020 05:16
0 votes 5 comments
Fail to set up conda environment for GATK with the gatkcondaenv.yml file
- fanwayne
- February 24, 2020 12:16
0 votes 5 comments
Problem running GenomeSTRiP CNVDiscovery on X chromosome
- Laura Cottino
- February 18, 2020 09:00
0 votes 5 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.