Germline

Forum thread to discuss GATK Germline tools

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
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
Missing RawGtCount annoation from GenotypeGVCF output
- Uday Evani
- January 21, 2023 01:23
- Edited
0 votes 19 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
The provided reference alleles do not appear to represent the same position, CTA* vs. CTT*
- Oliver Ruebenacker
- April 14, 2022 23:37
0 votes 16 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
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
GenomicsDBImport failing on 'conflicting field description'
- Alison Meynert
- September 11, 2020 16:11
0 votes 14 comments
Germline CNV WDL - SIGKILL
- stanedav
- June 01, 2020 07:21
0 votes 13 comments
Sortvcf generated empty file. GATK4
- Cecilia Kardum Hjort
- May 26, 2020 09:34
0 votes 13 comments
BQSR returns lower scores for male samples
- Mar Gonzàlez-Porta
- April 16, 2020 09:07
0 votes 13 comments
GATK4 validateSam Errors interpretation
- mehar
- February 02, 2021 22:23
0 votes 12 comments
Haplotype caller missed variant
- ensel
- May 28, 2020 10:37
0 votes 12 comments
GATK4 VariantAnnotator doesn't support AlleleBalance
- astrinaki_maria
- November 01, 2021 10:23
0 votes 11 comments
MarkduplicateSpark error
- Quentin Chartreux
- March 10, 2021 08:03
0 votes 11 comments
GenotypeGVCF by intervals
- @Anna
- December 10, 2020 14:25
0 votes 11 comments
Genome STRiP SV Preprocess
- Muhammad Shoaib Akhtar
- November 24, 2020 09:02
0 votes 11 comments
Bamout looks much worse than original BAM, false positive calls?
- Daniela Robles
- September 24, 2020 06:34
0 votes 11 comments
Genomestrip CNVdiscoverypipeline failed running paralleled
- lizhichao
- August 10, 2020 08:16
0 votes 11 comments
GATK 4.1.7.0 VariantAnnotator Processing Speed Drop
- danilovkiri
- May 07, 2020 15:55
- Edited
0 votes 11 comments
Error while running CreateReadCountPanelOfNormals
- Kate Pal
- February 25, 2020 17:51
- Edited
0 votes 11 comments
BAM file and VCF file showing different results
- DHWANI DHOLAKIA
- January 31, 2020 10:37
- Edited
0 votes 11 comments
Missing variant in VCF from GenotypeGVCFs
- James Abbott (Staff)
- January 14, 2020 10:53
0 votes 11 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.