New User Advice

DP for each variant bulk is skewed towards 50 and multiples of 50
- Lauren Fedenia
- April 21, 2021 19:02
0 votes 7 comments
GATK configration
- Wondessen Ayalew
- February 13, 2023 12:28
0 votes 5 comments
Markduplicates
- Atal Saha
- January 03, 2023 16:55
0 votes 5 comments
Estimate genotype proportions from filtered variants
- Daniel Castañeda Mogollón
- April 05, 2022 05:49
0 votes 5 comments
Running best practices workflow step-by-step in command line
- limetree
- June 04, 2021 05:12
1 vote 5 comments
How to provide custom exon-intron annotation source in Funcotator
- Elisabetta Manduchi
- February 18, 2022 13:48
0 votes 4 comments
GATK4.0.3.0 - CombineGVCFs - Unexpected base in allele bases
- HT
- October 01, 2021 05:28
0 votes 4 comments
Mutect2 wdl interval list and scatter count
- Sheryl
- March 06, 2023 02:19
- Edited
0 votes 3 comments
ApplyBQSR
- Wondessen Ayalew
- February 23, 2023 06:19
0 votes 3 comments
Help with running GATK RNAseq workflow with docker backend and multiple cpus?
- ThyagoLC
- September 02, 2021 15:38
- Edited
0 votes 3 comments
Is there a way to preserve numeric genotypes with VariantsToTable?
- Ben Sprung
- January 11, 2023 18:16
0 votes 2 comments
Scatter Gather principle by chromosome on Gatk
- Sushant Sawant
- November 28, 2022 06:44
- Edited
1 vote 2 comments
Where can I download Homo_sapiens_assembly38.haplotype_database.txt
- Sheryl
- November 17, 2022 05:36
0 votes 2 comments
Mutect2 somatic mutation calling for plant
- Lina Herliana
- September 15, 2021 01:42
0 votes 2 comments
Scatter / Gather for BaseRecalibrator on a single human WES dataset
- asg
- January 30, 2020 07:48
- Edited
0 votes 2 comments
MarkDuplicatesSpark Error
- Yosra Bejaoui
- February 08, 2023 06:25
0 votes 1 comment
Genotype and AD in Mutect2 vcf output
- Ester Feldmesser
- February 02, 2023 13:56
0 votes 1 comment
VariantFiltration Issue
- Ethan Mattice
- January 04, 2023 17:57
0 votes 1 comment
Multi-library designs: error proceeding from pre-processing to variant calling
- Sabrina McNew
- August 23, 2022 20:35
0 votes 1 comment
GenomicsDB Import issues
- aheritas
- July 15, 2022 15:47
0 votes 1 comment
Cromwell configuration problem: "No configuration setting found for key 'job-id-regex'"
- Joel Wallenius
- May 02, 2022 10:38
0 votes 1 comment
GenotypeGVCFs produces bizarre mapping quality distribution
- Daniel Nondorf
- November 18, 2021 16:49
0 votes 1 comment
GATK Non-model organism variant call SNP site all MQ same value
- Bekah W
- November 13, 2021 14:02
0 votes 1 comment
7 things I learned while reprocessing my WGS data on Terra: part 1
- KT Pickard
- June 14, 2021 21:49
0 votes 1 comment
Picard CheckIlluminaDirectory - Issue with file/folder structure?
- Jacob
- June 14, 2021 19:52
- Edited
0 votes 1 comment
Why doesn't haplotypecaller use PON?
- sinc
- June 04, 2021 05:11
0 votes 1 comment
Somatic Structure Variation on exome-seq data
- wiki97
- October 22, 2020 09:26
- Edited
0 votes 1 comment
Sensitive Copy Ratio Pipeline compatibility with tool "mergeLevels"
- Gannon Cottone
- May 06, 2020 15:34
0 votes 1 comment
Haplotype caller error "Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class"
- Anna Gatseva
- March 22, 2023 11:00
0 votes 0 comments
somatic CNV PoN
- Sheryl
- March 06, 2023 20:00
- Edited
0 votes 0 comments

Welcome

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.