Germline

Forum thread to discuss GATK Germline tools

Cohort_denoising.py parameter issue in GermlineCNVCaller Answered
- Sayal Guirales
- September 14, 2022 16:07
0 votes 15 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
Variant filtered from GVCF Answered
- LP
- June 14, 2022 14:15
1 vote 9 comments
Funcotator - all IGR classification Answered
- Noam Rudberg
- May 25, 2022 11:06
0 votes 10 comments
Funcotator Misconfigured Error (All IGR Annotations) Answered
- Gus Fridell
- May 20, 2022 21:31
0 votes 6 comments
DetermineGermlineContigPloidy error: line 137 Answered
- Carlos García Peral
- May 14, 2022 01:04
0 votes 3 comments
The same number of SNPS and INDELS identified for all samples after joint genotyping Answered
- Vincent Appiah
- April 21, 2022 22:34
- Edited
0 votes 12 comments
SelectVariants error: Multiple Criteria Answered
- Harini Prasanna
- April 19, 2022 17:07
0 votes 3 comments
B37 joint variant calling workflow says "for hg38 only" Answered
- Oliver Ruebenacker
- April 11, 2022 17:02
0 votes 1 comment
Program Record ID already in use in unmapped BAM file. Answered
- Oliver Ruebenacker
- March 31, 2022 21:19
0 votes 1 comment
Haplotypecaller 4.5.2.0 --alleles unexpected output Answered
- Geert Vandeweyer
- March 13, 2022 08:49
0 votes 7 comments
GenomicsDBImport error from # fields in AS_UNIQ_ALT_READ_COUNT Answered
- Jeff Gaither
- March 12, 2022 21:55
0 votes 3 comments
DetermineGermlineContigPloidy error with exome germline data Answered
- shun inoue
- March 02, 2022 04:25
- Edited
0 votes 5 comments
hs37d5 genome in the GATK bundle Answered
- Rea Kalampaliki
- February 17, 2022 10:16
- Edited
0 votes 3 comments
gatk GenotypeGVCFs produced an error Answered
- Lijun
- February 09, 2022 15:17
0 votes 7 comments
Difference in contigs between hg19_v0_Homo_sapiens_assembly19.fasta and hg19_v0_1000G_omni2.5.b37.vcf.gz and Mills_and_1000G_gold_standard.indels.hg19.sites.vcf files? Answered
- Rea Kalampaliki
- February 09, 2022 11:30
- Edited
0 votes 3 comments
Error while running CreateReadCountPanelOfNormals Answered
- Elizaveta Kolganova
- February 04, 2022 20:06
-1 votes 4 comments
GATK v4.2.4.0 VariantAnnotator running too slow Answered
- Anson Wong
- January 29, 2022 11:08
- Edited
0 votes 21 comments
HaplotypeCaller's -bamout created BAM-file not showing reads even with --force-active and --output-mode EMIT_ALL_ACTIVE_SITES Answered
- Vee Koo
- January 13, 2022 11:56
- Edited
0 votes 3 comments
Abnormal Results from GATK HaplotypeCaller --different variant Call from the fastq and its downsample fastq from the same fastqdata Answered
- Amy zhang
- January 12, 2022 08:29
- Edited
0 votes 8 comments
selectvariants error when consolidating GVCFs Answered
- jingchun liu
- December 14, 2021 03:08
- Edited
0 votes 3 comments
FilterVariantTranches Error: 'no variants with INFO score key "CNN_2D"' Answered
- Cher Wei Yuan
- December 13, 2021 03:38
- Edited
1 vote 7 comments
Haplotypecaller yields none mutation records Answered
- zhexin liu
- December 07, 2021 15:19
0 votes 1 comment
Error using FindBreakpointEvidenceSpark Answered
- Heba B abusamra
- December 06, 2021 07:18
0 votes 7 comments
GATK:CNV calling pipeline: error at step "GermlineCNVCaller program": org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException: python exited with 139 Answered
- Dr N Ch
- December 02, 2021 03:02
0 votes 3 comments
Combine GVCFs Answered
- Priyadarshini Thirunavukkarasu
- November 16, 2021 15:07
0 votes 6 comments
Values for InbreedingCoeff annotation not detected for ANY training variant Answered
- chenglei
- November 11, 2021 15:25
0 votes 6 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.