Germline

Forum thread to discuss GATK Germline tools

erro in VQSR (WGS)
- JUN ZHOU
- February 06, 2023 16:02
0 votes 1 comment
Has too many alleles in the combined VCF record
- rq m
- February 03, 2023 21:01
0 votes 1 comment
FastaAlternateReferenceMaker creating chimera
- Puechmaille
- February 01, 2023 15:00
0 votes 1 comment
variant calling: dict and indexing
- Nagarajan Raju
- February 05, 2023 14:23
0 votes 1 comment
Missing RawGtCount annoation from GenotypeGVCF output
- Uday Evani
- January 21, 2023 01:23
- Edited
0 votes 5 comments
GATK gCNV Calling pipeline error
- Heejun Jang
- January 27, 2023 08:56
0 votes 0 comments
PostprocessGermlineCNVCalls extremely slow after JointGermlineCNVSegmentation and produces many artifacts on sexual chromosomes
- Tintest
- December 06, 2022 14:51
- Edited
0 votes 1 comment
genomicsDBImport .A USER ERROR has occurred: Failed to create reader from file Answered
- Jennifer Irving-McGrath
- January 23, 2020 16:58
0 votes 9 comments
DetermineGermlineContigPloidy with exome germline data Answered
- S. Kose
- August 13, 2021 15:17
- Edited
0 votes 24 comments
Unable to trim uncertain bases without flow order information
- Laura Sanz
- December 21, 2022 02:41
- Edited
0 votes 0 comments
How to get a SNPs file for chicken genome to be used for base-quality score recaliberation step of GATK variant calling
- Mohamed Samir
- December 20, 2022 12:44
0 votes 0 comments
GenotypeGVCFs : VariantQueryProcessorException
- Henri-Jean Garchon
- November 29, 2022 10:55
0 votes 5 comments
HaplotypeCaller interval list
- Leo B
- October 18, 2022 10:35
0 votes 1 comment
PostprocessGermlineCNVCalls generate a segment file with missing GT field for the segment file
- NawarDalila
- November 09, 2022 13:07
0 votes 3 comments
Howto call germline SNPs from reads with MAPQ=0
- LH LV
- December 01, 2022 09:22
0 votes 0 comments
Varinat PASS given Genotype quality = 0
- Matteo Orlandi
- November 14, 2022 14:05
0 votes 2 comments
Input configuration for GATK4-gCNV workflow on Terra Answered
- Seunghun Han
- September 15, 2021 16:35
0 votes 5 comments
humanG1Kv37 (b37) to hg38 liftover issues
- Nienke Biesot
- February 23, 2021 12:17
0 votes 6 comments
JointGenotyping.ImportGvcfs terminates without an active exception
- Elizabeth Lee
- October 19, 2022 17:47
0 votes 4 comments
gCNV SVLEN question
- Adriana
- August 12, 2022 15:15
0 votes 4 comments
Cohort_denoising.py parameter issue in GermlineCNVCaller Answered
- Sayal Guirales
- September 14, 2022 16:07
0 votes 15 comments
Jointgenotyping Genomicsdbimport failed for no obvious reasons
- Jason Ni
- October 13, 2022 15:16
- Edited
1 vote 1 comment
CombineGVCFs 4.1.2.0 throws "java.lang.IllegalArgumentException: Features added out of order:" Answered
- Yokofakun
- March 17, 2020 09:13
0 votes 9 comments
CNNScoreVariants ImportError: cannot import name 'Adam' Answered
- albert son
- August 17, 2022 21:10
1 vote 1 comment
should I worry if the tmp folder not empty after completing GenotypeGVCFs Answered
- Jue Jiang
- August 11, 2022 12:08
0 votes 1 comment
Inconsistency between intervals.vcf and Normalized Copy ratios txt file in GCNV workflow 4.2.6.1 Answered
- SkyWarrior
- July 30, 2022 16:32
0 votes 12 comments
BaseRecalibrator tool recalibration table Answered
- Sharon Natasha Cox
- July 25, 2022 10:40
0 votes 1 comment
GATK concordance Answered
- Priyadarshini Thirunavukkarasu
- November 11, 2021 11:08
- Edited
0 votes 13 comments
CombineVariants Doesnt produce output
- nroak
- July 14, 2022 20:09
0 votes 1 comment
Funcotator - all IGR classification Answered
- Noam Rudberg
- May 25, 2022 11:06
0 votes 10 comments

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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.