New User Advice

Scatter Gather principle by chromosome on Gatk
- Sushant Sawant
- November 28, 2022 06:44
- Edited
1 vote 2 comments
Proper way to prepare .bam for MarkDuplicatesSpark Answered
- samuel
- July 06, 2022 06:46
1 vote 3 comments
Running best practices workflow step-by-step in command line
- limetree
- June 04, 2021 05:12
1 vote 5 comments
Genotype and AD in Mutect2 vcf output
- Ester Feldmesser
- February 02, 2023 13:56
0 votes 1 comment
Genome sequence analysis: preprocessing to variant analysis
- Nagarajan Raju
- January 24, 2023 16:13
0 votes 0 comments
Is there a way to preserve numeric genotypes with VariantsToTable?
- Ben Sprung
- January 11, 2023 18:16
0 votes 2 comments
VariantFiltration Issue
- Ethan Mattice
- January 04, 2023 17:57
0 votes 1 comment
Markduplicates
- Atal Saha
- January 03, 2023 16:55
0 votes 5 comments
Where can I download Homo_sapiens_assembly38.haplotype_database.txt
- Sheryl
- November 17, 2022 05:36
0 votes 2 comments
Unclear why Picard ValidateSamFile is producing an error Answered
- LOIC TALIGNANI
- November 15, 2022 09:51
0 votes 6 comments
CollectSamErrorMetrics error Answered
- Joe Georgeson
- October 10, 2022 17:41
0 votes 3 comments
no gatk installation
- pedro toruno
- October 04, 2022 19:18
0 votes 0 comments
VariantFiltration issue Answered
- Theresa Saunders
- September 09, 2022 20:41
0 votes 3 comments
Multi-library designs: error proceeding from pre-processing to variant calling
- Sabrina McNew
- August 23, 2022 20:35
0 votes 1 comment
Find rate of homozygosity Answered
- Joyce Anon
- July 28, 2022 05:12
0 votes 4 comments
GenomicsDB Import issues
- aheritas
- July 15, 2022 15:47
0 votes 1 comment
Package ‘gsalib’ was removed from the CRAN repository. Answered
- igor
- July 13, 2022 15:56
0 votes 3 comments
A USER ERROR has occurred: Contig chr1_KI270762v1_alt not present in reads sequence dictionary Answered
- Maha Tageldein
- June 06, 2022 05:03
0 votes 5 comments
GenomicsDBImport - why "intervals" is required?? Answered
- Jianying Li
- May 25, 2022 00:39
0 votes 3 comments
Gatk4 rnaseq germline snps indels json file Answered
- Alan Foley
- May 19, 2022 10:29
- Edited
0 votes 3 comments
Variant Quality Score Recalibration Answered
- Jakub S
- May 09, 2022 15:27
0 votes 3 comments
How to use WGA Data in picard Answered
- Marcus Varni
- May 03, 2022 23:13
0 votes 3 comments
Suggestions to find pathogenic variant Answered
- Joyce Anon
- May 03, 2022 20:57
0 votes 4 comments
Cromwell configuration problem: "No configuration setting found for key 'job-id-regex'"
- Joel Wallenius
- May 02, 2022 10:38
0 votes 1 comment
Error, ShouldNeverReachHereException, FuncotationMap in FilterFuncotations Answered
- Joyce Anon
- April 25, 2022 06:30
0 votes 20 comments
GATK working, but -ERC command not found Answered
- Ann W
- April 12, 2022 15:06
0 votes 3 comments
Somatic mutation detection in HLA regions using hg38 alt-aware alignments Answered
- Elisabetta Manduchi
- April 12, 2022 15:00
0 votes 2 comments
ReadsPipelineSparkMulticore.wdl, Unrecognized runtime attribute keys: discs, cpu Answered
- Andrew Erzunov
- April 19, 2022 20:40
- Edited
0 votes 13 comments
Proper references for mutec2 working in tumour-only mode Answered
- Dr Andrzej Kubiak
- April 05, 2022 11:21
0 votes 1 comment
Estimate genotype proportions from filtered variants
- Daniel Castañeda Mogollón
- April 05, 2022 05:49
0 votes 5 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.