Germline

Forum thread to discuss GATK Germline tools

[Repost] ReadGroup missing when Applying BQSR Answered
- Robinn Teoh
- January 06, 2021 23:35
0 votes 44 comments
Hg38 RNAseq germline variant calling – BQSR steps Answered
- manolis
- January 17, 2021 11:43
- Edited
0 votes 43 comments
Funcotator Error, incompatible contigs Answered
- J LoPiccolo
- September 28, 2021 23:41
0 votes 35 comments
memory troubles and modified imports for pipeline running on Google Cloud
- gouret
- March 02, 2021 10:47
0 votes 34 comments
How do I SelectVariants from GenomicsDB stored in GCS?
- Lucas Taniguti
- January 31, 2021 13:04
1 vote 27 comments
MarkDuplicatesSpark consumes enormous amount of RAM Answered
- Yangyxt
- March 11, 2020 02:20
1 vote 25 comments
DetermineGermlineContigPloidy with exome germline data Answered
- S. Kose
- August 13, 2021 15:17
- Edited
0 votes 24 comments
GATK v4.2.4.0 VariantAnnotator running too slow Answered
- Anson Wong
- January 29, 2022 11:08
- Edited
0 votes 21 comments
erro running "gatk seq-format-validation workflow"
- zdr j
- July 14, 2020 05:30
0 votes 21 comments
HaplotypeCaller error: Read is malformed: read starts with deletion
- Sue John
- March 05, 2020 10:41
1 vote 21 comments
DP/AD in SNP greater than coverage in bamout?
- mk
- May 11, 2020 08:32
0 votes 20 comments
"Did not inflate expected amount" Error Answered
- Jacob Wang
- November 02, 2021 08:27
0 votes 18 comments
"htsjdk.samtools.SAMFormatException: Invalid GZIP header" in VariantRecalibrator Answered
- zhaol
- October 13, 2020 14:17
- Edited
0 votes 18 comments
.GenomicsDBException: Duplicate sample name found:
- Charles H. Langley
- September 01, 2020 21:42
0 votes 17 comments
Strategy for buildling GenomicsDB
- Bernt Guldbrandtsen
- February 27, 2020 15:05
0 votes 17 comments
Number of variants: discordance between HC and CNN
- manolis
- January 09, 2020 11:40
- Edited
0 votes 17 comments
combineGVCF errors and questions: inconsistent references & combineGVCF twice
- Mingzhou Fu
- August 17, 2021 16:09
0 votes 16 comments
Big variance of PCT_BASES_20X between software versions
- JonR
- June 30, 2020 17:00
0 votes 16 comments
Cohort_denoising.py parameter issue in GermlineCNVCaller Answered
- Sayal Guirales
- September 14, 2022 16:07
0 votes 15 comments
CombineGVCF on chrX and chrY hg38 running for ever
- mehar
- March 21, 2021 18:50
- Edited
0 votes 15 comments
GATK Funcotator and GATK VariantFiltration
- Amit
- January 15, 2020 22:58
0 votes 15 comments
The provided reference alleles do not appear to represent the same position, CTA* vs. CTT*
- Oliver Ruebenacker
- April 14, 2022 23:37
0 votes 14 comments
Errors in bam files Answered
- Priyadarshini Thirunavukkarasu
- September 23, 2021 13:48
0 votes 14 comments
Variant not called with HaplotypeCaller Answered
- flora ponelle
- May 31, 2021 09:01
0 votes 14 comments
Haplotypecaller : variant calling not seen in bamout alignments Answered
- fabienne JABOT-HANIN
- May 27, 2021 11:21
0 votes 14 comments
Bug in GATK4 variant calling followed by CalculateGenotypePosteriors Answered
- G E
- April 02, 2021 17:49
- Edited
0 votes 14 comments
GenomicsDBImport failing on 'conflicting field description'
- Alison Meynert
- September 11, 2020 16:11
0 votes 14 comments
BaseRecalibrator - no suitable codecs Answered
- Rhodri Smith
- April 01, 2020 09:59
1 vote 14 comments
Convert combineGVCF result to GenomicsDB [Repost] Answered
- Jing Yu
- February 13, 2020 12:45
- Edited
1 vote 14 comments
GATK concordance Answered
- Priyadarshini Thirunavukkarasu
- November 11, 2021 11:08
- Edited
0 votes 13 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.