Other

No results of CollectvariantCallingMetrics Answered
- Yenan
- November 30, 2020 07:13
0 votes 30 comments
Genome STRiP CNVDiscovery pipeline error
- Beilei Bian
- March 25, 2020 00:39
0 votes 27 comments
ValidateSamFile: New error after running BQSR
- ISmolicz
- November 16, 2020 15:21
0 votes 19 comments
How to run GenotypeConcordance
- Ana Marija
- September 12, 2020 00:57
- Edited
0 votes 19 comments
Broken: conda env create -n gatk -f gatkcondaenv.yml
- James White
- April 24, 2020 17:01
0 votes 17 comments
Problem Installing GATK python environment - SOLUTION POSTED! Featured
- SkyWarrior
- February 06, 2020 07:21
- Edited
1 vote 17 comments
Panel of Normals Documentation Answered
- Ryan Gimple
- April 16, 2020 17:48
1 vote 16 comments
filterSamReads stdout format error
- rcorbett
- February 04, 2021 15:31
- Edited
0 votes 15 comments
ERROR MESSAGE: No gender data for sample:sample7
- termius
- August 05, 2020 07:02
0 votes 15 comments
Fatal error occuring during GATK4 PathSeqPipeline tool run
- Jude Taylor
- July 14, 2020 12:40
0 votes 15 comments
MarkDuplicatesSparks not removing some duplicates?
- Tom Morrison
- June 18, 2020 14:55
0 votes 15 comments
DepthofCoverage GATK4.1.7.0 -gene-list Answered
- marta r
- May 27, 2020 14:19
0 votes 15 comments
Setting SPARK resources when using the gatk release version
- Ury Alon
- May 18, 2020 04:42
- Edited
0 votes 15 comments
Genomestrip preprocessing error
- chae chae
- March 08, 2022 03:41
- Edited
0 votes 13 comments
Error running FilterMutectCalls: alpha must be greater than 0 but got NaN
- Larry S
- September 20, 2020 14:48
0 votes 13 comments
--tmp-dir option user error Answered
- Brynjar Sigurðsson
- August 10, 2020 12:22
0 votes 13 comments
CNNScoreVariants carshes with java.lang.NullPointerException Answered
- riederd
- January 17, 2020 15:29
1 vote 13 comments
Any automatic downloadable gatk3?
- ale
- January 09, 2020 13:16
2 votes 13 comments
Error in running GenomicsDBConfigException Answered
- Shivangi Agarwal
- December 20, 2021 14:51
0 votes 12 comments
mitochondria_m2_wdl: MitochondriaPipeline Issues
- Valentin
- July 09, 2020 13:42
0 votes 12 comments
GATK4 HaplotypeCaller ERROR : expected haplotypes.size() >= eventsAtThisLoc.size() + 1
- Şevval Aktürk
- April 23, 2020 12:26
0 votes 12 comments
HaplotypeCaller complains (in 2 different ways) about sample-name
- Terry Jones
- February 18, 2020 14:07
0 votes 12 comments
Error in SplitNCigarReads
- Giulia Corsi
- August 19, 2020 15:26
0 votes 11 comments
Merge different individual VCF
- Linda Do
- July 06, 2020 07:05
1 vote 11 comments
FilterByOrientationBias vanished in 4.1.6.0
- riederd
- March 30, 2020 11:41
0 votes 11 comments
Does GATK4 BaseRecalibrator not understand relative paths?
- Eva (Evander)
- October 17, 2022 12:51
0 votes 10 comments
Error when trying to generate the second recalibration table for AnalyzeCovariates
- ISmolicz
- February 17, 2021 12:03
0 votes 10 comments
FixVcfHeader error: A reference dictionary is required for creating Tribble indices on the fly
- jorgez
- July 20, 2020 18:52
0 votes 10 comments
LiftoverVcf fails to lift over a GVCF file. Error java.lang.ArrayIndexOutOfBoundsException: -1
- jorgez
- May 06, 2020 12:54
0 votes 10 comments
GenomeStrip SVPreprocess works with for a chromosome region; but fail for whole genome Answered
- APato
- February 03, 2020 21:28
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.