Other

--tmp-dir option user error Answered
- Brynjar Sigurðsson
- August 10, 2020 12:22
0 votes 13 comments
GenomicsDBImport: Attempting to genotype more than 50 alleles Answered
- Nils Homer
- August 06, 2020 00:13
1 vote 9 comments
GenomicsDBImport: has too many genotypes in the combined VCF record
- Nils Homer
- August 06, 2020 00:12
- Edited
1 vote 2 comments
Discord / Slack group
- Saatvig Patel
- August 05, 2020 16:39
0 votes 1 comment
ERROR MESSAGE: No gender data for sample:sample7
- termius
- August 05, 2020 07:02
0 votes 15 comments
Error: Invalid or corrupt jarfile cromwell-52.jar
- Saatvig Patel
- July 27, 2020 10:07
0 votes 3 comments
Speeding up GATK4 DepthOfCoverage
- Michael Franklin
- July 27, 2020 02:11
0 votes 2 comments
SelectVariants error
- Rajul Tayal
- July 25, 2020 09:12
- Edited
0 votes 1 comment
Dosages with Mutect2
- Leore Nehemie Bensabath
- July 24, 2020 08:36
0 votes 6 comments
GATK mark duplicates error
- Kshama Aswath
- July 22, 2020 20:26
- Edited
0 votes 2 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
Unable to load library 'lsf': liblsf.so: and Unable to submit job: denied(CNVdiscovery)
- termius
- July 19, 2020 14:40
0 votes 3 comments
How to set the length when make a mask fasta file for Glycine_max.Glycine_max_v2.0.dna.fa
- termius
- July 17, 2020 08:45
0 votes 2 comments
run SVPreprocess and SVGenotyper for each sample
- zzq
- July 16, 2020 04:10
0 votes 7 comments
Variable region not considered active region by HaplotypeCaller
- Veronica
- July 15, 2020 22:19
0 votes 1 comment
Fatal error occuring during GATK4 PathSeqPipeline tool run
- Jude Taylor
- July 14, 2020 12:40
0 votes 15 comments
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
mitochondria_m2_wdl: MitochondriaPipeline Issues
- Valentin
- July 09, 2020 13:42
0 votes 12 comments
RealignerTargetCreator
- Madza Farias-Virgens
- July 07, 2020 20:01
0 votes 2 comments
Confusing GVCF results Answered
- Yue Wang
- July 07, 2020 14:31
- Edited
0 votes 1 comment
Warning: Reading will be unbuffered. Answered
- Linda Do
- July 06, 2020 16:35
1 vote 3 comments
Merge different individual VCF
- Linda Do
- July 06, 2020 07:05
1 vote 11 comments
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
How to reduce the processing time of BwaMemIndexImageCreator Answered
- Ganesh P Kumar
- June 25, 2020 07:10
0 votes 2 comments
SelectVariants to get a vcf file with 1 individual from a vcf file with 3 individuals
- Linda Do
- June 22, 2020 21:46
0 votes 3 comments
Picard LiftOverVCF 2.22.3. hs37d5_to_GRCh38. Many mismatched reference alleles
- Argonaut44
- June 23, 2020 18:09
- Edited
0 votes 4 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.