Other

CalculateContamination Sample Source
- gufran
- November 25, 2020 15:30
- Edited
0 votes 1 comment
MarkDuplicates has different duplication metrics than EstimateLibraryComplexity
- Ravi Mandla
- November 21, 2020 01:09
0 votes 1 comment
Rename sample in vcd.idx file
- Vilde Bruhn
- November 12, 2020 10:15
0 votes 1 comment
genotype 0/0 if not SNPs identified by GATK
- ZYou
- October 20, 2020 17:22
0 votes 1 comment
Old forum posts about FireCloud
- Kathleen Morrill
- October 04, 2020 16:26
0 votes 1 comment
Unable to create iterator for rod named variant
- dexianghu
- October 03, 2020 14:18
0 votes 1 comment
Error using liftovervcf to do hg18tohg19
- Scarlett
- September 28, 2020 17:34
0 votes 1 comment
Threads parameters of Depth of coverage (GATK4.1.7.0 beta version)
- Henry
- September 11, 2020 06:16
- Edited
0 votes 1 comment
FuncotatorDataSourceDownloader does not download latest version?
- A. Brink
- September 10, 2020 13:50
0 votes 1 comment
Weird parameter of Depth of coverage (GATK4.1.7.0 beta version)
- Henry
- September 11, 2020 06:05
- Edited
0 votes 1 comment
Where and how I can get GenomeAnalysisTK.jar script?
- Ana Marija
- September 04, 2020 22:35
0 votes 1 comment
gatk-4.1.8.1/ValidateVariants - bypass contig length check?
- Matthew Maher
- September 03, 2020 15:44
0 votes 1 comment
Error on FastaAlternateReferenceMaker process
- JaeJun Lee
- September 03, 2020 06:09
0 votes 1 comment
CombineVariants set attribute filters on all callers explicitly (not with filteredInAll)
- jorgez
- September 01, 2020 11:41
0 votes 1 comment
GenotypeGVCFs stops halfway through scaffold - java.lang.NullPointerException
- Peter Euclide
- August 29, 2020 14:16
0 votes 1 comment
HaplotypeCaller produces variant lines with no depth information when calling gvcf
- Berk Gonenc
- August 22, 2020 14:27
0 votes 1 comment
How to make a 1kg_ref_panel_v1.ped?
- 2tong
- August 11, 2020 02:09
- Edited
0 votes 1 comment
Discord / Slack group
- Saatvig Patel
- August 05, 2020 16:39
0 votes 1 comment
SelectVariants error
- Rajul Tayal
- July 25, 2020 09:12
- Edited
0 votes 1 comment
Variable region not considered active region by HaplotypeCaller
- Veronica
- July 15, 2020 22:19
0 votes 1 comment
FilterMutectCalls failing filters
- Elizabeth Schabot
- July 13, 2020 20:57
0 votes 1 comment
WDL RNA-seq Hisat2
- Thinh B. Vo
- July 13, 2020 19:24
0 votes 1 comment
How to execute workflow locally without docker
- jiawei
- July 11, 2020 15:28
0 votes 1 comment
Confusing GVCF results Answered
- Yue Wang
- July 07, 2020 14:31
- Edited
0 votes 1 comment
Extract individual samples from combined gvcf file
- Balat
- July 03, 2020 01:20
0 votes 1 comment
Inquiry about the GATK Best Practices for variant calling on RNAseq
- Benjamin Hing
- July 02, 2020 00:24
0 votes 1 comment
gatk3-register
- touyupang
- July 01, 2020 05:23
0 votes 1 comment
resource bundle b37
- hirokomatsui
- June 19, 2020 00:20
0 votes 1 comment
IlluminaBasecallsToSam - barcode was not expected
- Vincent Hahaut
- June 10, 2020 19:04
0 votes 1 comment
When will AnalyzeCovariates support R/4.0
- Qi Yu
- June 09, 2020 21:20
0 votes 1 comment

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.