Other

Loss of data after HaplotypeCaller
- mbesskd5
- February 14, 2020 10:14
- Edited
0 votes 5 comments
ShiftFasta creates empty intervals file Answered
- Ram
- October 21, 2022 07:56
- Edited
0 votes 4 comments
How can I build the GATK jar so that the intel native libraries are available? Answered
- Mark Schreiber
- September 22, 2022 16:49
0 votes 4 comments
libgkl_compression.so not found + Failed to detect Google Compute Engine in a GATK workflow Answered
- Marta Giovalli
- September 14, 2022 12:47
- Edited
0 votes 4 comments
Haploytpe caller shows me that 0 read(s) were filtered by: MappingQualityAvailableReadFilter etc. Answered
- pb
- July 13, 2022 14:15
0 votes 4 comments
Refseq accession number and version number in Funcotator Answered
- TMB
- April 26, 2022 04:13
0 votes 4 comments
vulnerability issue for gatk-package-4.2.5.0-local.jar Answered
- John Yu
- March 09, 2022 14:27
0 votes 4 comments
Running Genome STRiP SVPreprocess, but I got error message: "Invalid command line: Malformed walker argument: Could not find walker with name: ComputeInsertSizeHistogramsWalker"
- Norio Tanaka
- June 15, 2021 14:22
0 votes 4 comments
How to merge approx 150 bam file using Picard
- Abrish
- December 27, 2020 14:02
0 votes 4 comments
DepthOfCoverage in GATK4.1.9.0 with -gene-list option
- David Jaspez
- December 21, 2020 17:36
- Edited
0 votes 4 comments
MitochondriaPipeline on merged Bams
- Valentin
- November 12, 2020 11:05
0 votes 4 comments
Interval Filtering -- How does it actually work?
- Alijah O'Connor
- September 21, 2020 22:54
- Edited
0 votes 4 comments
Picard LiftOverVCF 2.22.3. hs37d5_to_GRCh38. Many mismatched reference alleles
- Argonaut44
- June 23, 2020 18:09
- Edited
0 votes 4 comments
Picard CollectHsMetrics PCT_EXC_OFF_TARGET
- Holly Corbitt
- May 07, 2020 04:09
1 vote 4 comments
A USER ERROR has occurred: Number of read groups must be >= 1, but is 0
- Jay Singh
- May 01, 2020 17:24
0 votes 4 comments
Do I need to perform fastqc and adapters trimming before gatk pipeline?
- LG
- May 01, 2020 02:49
2 votes 4 comments
ValidateSamFile tmp not found ERROR with not output or Exception
- James
- April 20, 2020 23:34
0 votes 4 comments
Picard ExtractIlluminaBarcodes return NullPointerException error
- Jing Lin
- March 20, 2020 21:52
0 votes 4 comments
Do BQSR ignore VCF sites marked as filtered, or must they be removed from the file?
- mk
- March 11, 2020 00:37
0 votes 4 comments
Question: Picard - MergeBamAlignment: Reads remaining on alignment iterator
- Nguyen Nguyen Thanh
- February 23, 2020 15:03
0 votes 4 comments
HaplotypeCaller produces very large .idx files
- Anze Staric
- February 20, 2020 20:30
1 vote 4 comments
WES covarage analysis
- Surdan Burasi
- February 16, 2020 21:09
0 votes 4 comments
HaplotypeCaller confuses introns as long deletions
- Vladimir Souza
- November 09, 2022 23:03
- Edited
0 votes 3 comments
Error in Running command CreateExtendedIlluminaManifest Answered
- Nur Adlina Binti Mohd Affian
- October 03, 2022 09:21
0 votes 3 comments
How to run muTect without normal sample? Answered
- Yingjie Zhu
- July 11, 2022 21:35
1 vote 3 comments
markDuplicatesSpark running out of memory Answered
- Matt Snyder
- June 09, 2022 19:34
0 votes 3 comments
GATK R plots with R v4.1.2 Answered
- Franz Gassner
- January 24, 2022 09:36
0 votes 3 comments
markduplicatesSpark .bam.parts output error (directory already exists) Answered
- Morgan Sparks
- September 30, 2021 16:31
0 votes 3 comments
GenomeSTRiP SVPreprocess failed Answered
- Jenny Xu
- July 27, 2021 02:46
0 votes 3 comments
LiftoverVcf: hg19 to hg38 all variants mismatched
- Ken Hanscombe
- February 17, 2021 14:13
0 votes 3 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.