Other

Liftover Picard hg19 to hg38: variants were not successfully lifted over
- Andres Caballero
- December 09, 2022 18:39
2 votes 2 comments
Do I need to perform fastqc and adapters trimming before gatk pipeline?
- LG
- May 01, 2020 02:49
2 votes 4 comments
Out of memory error using OpenJDK vs Oracle JDK for CNV-LOH
- Jose Arcadio Buendia
- February 28, 2020 01:53
- Edited
2 votes 2 comments
Any automatic downloadable gatk3?
- ale
- January 09, 2020 13:16
2 votes 13 comments
GenomeSTRiP SVPreprocess error
- Jibin Jeong
- September 15, 2022 04:51
- Edited
1 vote 1 comment
Genomestrip: Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing
- Senwei
- April 27, 2022 07:59
1 vote 2 comments
HaplotypeCaller -ERC GVCF -variant_index_type LINEAR
- Matilde
- January 22, 2021 18:22
1 vote 1 comment
How do I rename output folder created using glob (WDL-Cromwell)?
- Mar Quiroga
- November 25, 2020 23:20
1 vote 1 comment
GenomicsDBImport: has too many genotypes in the combined VCF record
- Nils Homer
- August 06, 2020 00:12
- Edited
1 vote 2 comments
Merge different individual VCF
- Linda Do
- July 06, 2020 07:05
1 vote 11 comments
Picard CollectHsMetrics PCT_EXC_OFF_TARGET
- Holly Corbitt
- May 07, 2020 04:09
1 vote 4 comments
Problem Installing and testing GATK-4.1.7.0
- Arjun Upadhaya
- May 04, 2020 06:34
1 vote 5 comments
jar for mutect 1.1.7
- Knight Ni
- April 19, 2020 17:08
1 vote 6 comments
GATK/Picard does not detect mates in paired-end BAM
- jipvdinter
- April 07, 2020 11:34
- Edited
1 vote 3 comments
HaplotypeCaller produces very large .idx files
- Anze Staric
- February 20, 2020 20:30
1 vote 4 comments
ValidateSamFile behavior
- Robert Edgar
- February 17, 2020 18:07
1 vote 7 comments
Problem Installing GATK python environment - SOLUTION POSTED! Featured
- SkyWarrior
- February 06, 2020 07:21
- Edited
1 vote 17 comments
Typos in docs
- Andrea Haessly
- January 29, 2020 20:47
1 vote 1 comment
MarkDuplicatesSpark crash
- David Gómez-Sánchez
- January 07, 2020 17:02
1 vote 10 comments
Question about the allele depth generated by haplotypecaller and ASEReadCounter
- 杨烁
- March 27, 2023 09:00
0 votes 0 comments
FastaAlternateReferenceMaker generates same sequence for multisample vcf
- Kathrin B
- March 17, 2023 14:09
0 votes 0 comments
GATK ContaminationModel
- Itai Beno
- March 15, 2023 16:36
0 votes 0 comments
Error while running HaplotypeCaller
- Achint Kumar
- February 19, 2023 13:54
0 votes 1 comment
Picard LiftOver behaviour for multiallelic positions
- Adeline Morez
- February 03, 2023 11:22
0 votes 1 comment
ASEReadCounter does not return the value only for chrX
- Kei Enomoto
- February 04, 2023 05:07
- Edited
0 votes 2 comments
ApplyVQSR: "[W::bgzf_read_block] EOF marker is absent" and "[tabix] the index file exists." errors
- Bob Ye
- January 25, 2023 23:12
0 votes 0 comments
gatk4-GenotypeGVCFs.nf doens't recognize Primary_000001F chromosomes for process GatherVcfs
- Carole Couture
- December 08, 2022 15:19
0 votes 0 comments
HaplotypeCaller confuses introns as long deletions
- Vladimir Souza
- November 09, 2022 23:03
- Edited
0 votes 3 comments
error when running ASEReadCounter
- behzad
- October 27, 2022 11:20
0 votes 2 comments
SortSam - Question about I/O error
- Henry
- October 27, 2022 08:20
0 votes 2 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.