Other

Base Recalibrator " No Positional Argument is defined for this tool"
- megha thippanna
- January 27, 2023 05:40
0 votes 0 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
Picard LiftOverVCF 2.22.3. hs37d5_to_GRCh38. Many mismatched reference alleles
- Argonaut44
- June 23, 2020 18:09
- Edited
0 votes 4 comments
Liftover Picard hg19 to hg38: variants were not successfully lifted over
- Andres Caballero
- December 09, 2022 18:39
2 votes 2 comments
HaplotypeCaller confuses introns as long deletions
- Vladimir Souza
- November 09, 2022 23:03
- Edited
0 votes 3 comments
gatk4-GenotypeGVCFs.nf doens't recognize Primary_000001F chromosomes for process GatherVcfs
- Carole Couture
- December 08, 2022 15:19
0 votes 0 comments
Invalid or corrupt jarfile error Answered
- Benjamin Singer
- November 30, 2022 00:55
- Edited
0 votes 2 comments
Does GATK4 BaseRecalibrator not understand relative paths?
- Eva (Evander)
- October 17, 2022 12:51
0 votes 10 comments
CombineGVCFs - possible to restart/continue run?
- medgen
- October 11, 2022 14:01
0 votes 5 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
Broken: conda env create -n gatk -f gatkcondaenv.yml
- James White
- April 24, 2020 17:01
0 votes 17 comments
ShiftFasta creates empty intervals file Answered
- Ram
- October 21, 2022 07:56
- Edited
0 votes 4 comments
Error in Running command CreateExtendedIlluminaManifest Answered
- Nur Adlina Binti Mohd Affian
- October 03, 2022 09:21
0 votes 3 comments
Accessing the resource bundle. Answered
- nagam surya
- June 28, 2022 18:35
0 votes 6 comments
CGA3_WES_Characterization_Pipeline_v0.2_Jun2019 PoN Errors...
- Rose Gold
- September 28, 2022 14:32
0 votes 1 comment
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
How to run muTect without normal sample? Answered
- Yingjie Zhu
- July 11, 2022 21:35
1 vote 3 comments
GenomeSTRiP SVPreprocess error
- Jibin Jeong
- September 15, 2022 04:51
- Edited
1 vote 1 comment
VCF input example Answered
- Noam Rudberg
- August 07, 2022 09:45
0 votes 1 comment
GenomicsDBImport: Attempting to genotype more than 50 alleles Answered
- Nils Homer
- August 06, 2020 00:13
1 vote 9 comments
Cannot use haplotype caller on STAR-aligned data Answered
- David Condon
- August 05, 2022 15:49
0 votes 2 comments
MergeVcfs issue: Illegal character in fragment at index 1: ##fileformat=VCFv4.2 Answered
- Liyang Zhang
- August 03, 2022 08:02
- Edited
0 votes 1 comment
FindBadGenomicKmersSpark running indefinitely Answered
- Cher Wei Yuan
- August 02, 2022 02:25
0 votes 5 comments
Using the IndexFeatureFile, doesn't recognize -F flag Answered
- Gijs C
- July 30, 2022 12:21
0 votes 2 comments
GenomicsDBImport works in interactive shell, but not in a script Answered
- Guy Shapira
- July 21, 2022 22:05
0 votes 1 comment
Haploytpe caller shows me that 0 read(s) were filtered by: MappingQualityAvailableReadFilter etc. Answered
- pb
- July 13, 2022 14:15
0 votes 4 comments
MarkduplicatesSpark failed Answered
- lid.zigh
- November 23, 2021 13:44
0 votes 5 comments
MarkDuplicatesSpark crash
- David Gómez-Sánchez
- January 07, 2020 17:02
1 vote 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.