Special GATK Use Cases

Information here covers items that are not in Best Practices but may someday be a part of Best Practices

Using Mutect2 on Mac M1
- Ieuan Walker
- February 01, 2023 09:50
1 vote 0 comments
How do I know why gatk is removing some of my reads for geotyping?
- Alicia Hernandez
- January 25, 2023 06:26
0 votes 0 comments
java.lang.NullPointerException error in VariantQC
- ankita lawarde
- January 17, 2023 13:15
0 votes 3 comments
DepthOfCoverage gives ~100% coverage for ultra-deep sequencing data
- Mitsuko Korobkin
- November 23, 2022 13:32
- Edited
0 votes 3 comments
VariantsToTable cannot deal with deletion correctly
- Yating Liu
- November 11, 2022 19:48
- Edited
0 votes 2 comments
variant calling with allotetraploid species
- Giuseppe Aprea
- November 10, 2022 14:16
0 votes 1 comment
HaplotypeCaller does not work Answered
- Aziz
- October 05, 2022 02:20
0 votes 2 comments
use_jdk_deflater not defined?
- antoine chaillon
- October 01, 2022 19:36
0 votes 1 comment
Can I swap the identities of the tumour and the normal samples to reverse verify the authenticity of the detected variants?
- Di Pan
- September 22, 2022 16:10
0 votes 1 comment
Using gatk VariantFiltration to filter ONT wf-artic generated VCF files
- rohit satyam
- September 07, 2022 12:40
- Edited
0 votes 5 comments
Read Group (UNKNOWN) is not a recognized platform
- qianqiu zu
- September 06, 2022 08:46
- Edited
1 vote 1 comment
Select allele based on phased genotype while generating consensus sequence
- Upamanyu Ghose
- September 01, 2022 09:22
0 votes 1 comment
CombineGVCFs - elements of input iterator not sorted Answered
- Artamir
- August 29, 2022 11:52
0 votes 2 comments
gatk CombineGVCFs Answered
- Hanying
- August 29, 2022 05:11
0 votes 2 comments
BaseRecaliberator .fai file error
- nasim
- August 17, 2022 17:44
0 votes 1 comment
RAD-seq Variant calling
- Rafet Al
- August 03, 2022 21:45
0 votes 1 comment
GATK error Answered
- Roohollah Kheiri
- August 01, 2022 11:12
0 votes 4 comments
GATK HaplotypeCaller issues with Genotyping (GT)
- pb
- July 20, 2022 12:21
- Edited
0 votes 3 comments
HaplotypeCaller output not generated, no error Answered
- Neharika Singh
- July 17, 2022 20:34
0 votes 1 comment
DepthOfCoverage Output Files Empty - mtDNA
- Rachel Shadoff
- July 15, 2022 00:30
0 votes 1 comment
incomplete output when running ASEReadCounter Answered
- behzad
- July 13, 2022 14:17
0 votes 5 comments
Is "Somatic short variant discovery" the correct Pipeline to identify differential microsatellites? Answered
- Arye Harel
- June 23, 2022 11:41
0 votes 6 comments
Monomorphic sites after GenotypeGVCFs --include-non-variant-sites Answered
- Diana Robledo
- June 23, 2022 10:56
0 votes 8 comments
HaplotypeCaller not writing output Answered
- Science Matters
- June 16, 2022 13:02
0 votes 1 comment
--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' Answered
- Roohollah Kheiri
- June 15, 2022 18:41
0 votes 1 comment
Standalone HaplotypeCaller Answered
- Pryce Turner
- June 09, 2022 23:14
0 votes 5 comments
Genotype concordance - dictionaries are not the same size Answered
- Jennifer Schulze
- June 07, 2022 10:04
0 votes 1 comment
java.lang.ArrayIndexOutOfBoundsException: 32770 while using GenotypeGVCFs Answered
- Akshaya Vasudevan
- June 01, 2022 16:12
- Edited
0 votes 1 comment
Find variants with HaplotypeCaller on MAPQ0 regions
- Sylvain Brohee
- May 31, 2022 13:58
0 votes 1 comment
no read counts per allele while using gatk ASEReadCounter Answered
- behzad
- June 08, 2022 09:23
- Edited
0 votes 11 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.