Documentation Questions

GATK Best Practices Mitochondrial Analysis Answered
- ajwils
- January 09, 2020 21:15
- Edited
1 vote 45 comments
mutect2 multi-sample Answered
- zhao shilin
- May 07, 2020 17:27
- Edited
0 votes 35 comments
QualByDepth documentation issue Answered
- Uday Evani
- September 09, 2020 21:38
0 votes 18 comments
CollectAllelicCounts interval_list Answered
- jejacobs23
- May 18, 2020 22:33
1 vote 15 comments
GenotypeGVCFs only accepts single combinedGVCF? CombineGVCFs & genomicsdb errors... .interval_list subset Answered
- Mingzhou Fu
- July 29, 2021 22:42
0 votes 12 comments
How does Mutect2 count read depth/coverage? Answered
- Sameer Shankar
- February 16, 2023 20:40
1 vote 11 comments
haplotypeCaller phasing Answered
- Jeremie Kalfon
- October 05, 2021 15:07
- Edited
0 votes 11 comments
Interpretation of gene_summary output from DepthofCoverage Answered
- neethukrishna Kausthubham
- August 26, 2021 11:08
0 votes 11 comments
Germline sites in Mutect2 Answered
- G E
- March 19, 2021 04:39
- Edited
0 votes 11 comments
germline-resource Answered
- Juechen Yang
- March 17, 2020 17:32
0 votes 10 comments
GenomAD files for MuTect2 Answered
- Felix
- May 06, 2020 10:18
0 votes 9 comments
GenomicsDBImport -L [string] (but for the whole genome): purpose to generate invariant sites Answered
- Pete Thorpe
- January 20, 2022 08:51
0 votes 8 comments
Difference between GATK Germline CNV Pipeline vs Genome STRiP? Answered
- Muhammad Shoaib Akhtar
- October 29, 2020 08:49
0 votes 8 comments
Documentation for running GATK and Cromwell on IBM Cloud Answered
- Takeshi Yoshimura
- April 05, 2022 01:24
1 vote 7 comments
picard sortvcf: what does it do? Answered
- Thomas Juettemann
- November 09, 2021 17:31
0 votes 7 comments
FilterFuncotations Duplicate key error Answered
- Azza Ahmed
- October 14, 2021 10:53
0 votes 7 comments
Where is the list of annotations and annotation groups? Answered
- tedtoal
- July 05, 2021 23:05
2 votes 7 comments
MTLowHeteroplasmyFilterTool documentation Answered
- jorgez
- June 11, 2021 12:58
0 votes 7 comments
Calculation method of the global_read_depth.tsv file of the DetermineGermlineContigPloidy tool Answered
- Tintest
- May 20, 2021 14:35
0 votes 7 comments
Alt Contig tutorial question Answered
- Linda Do
- March 15, 2021 05:22
0 votes 7 comments
Three questions about calling CNV in Germline. Answered
- rq m
- March 12, 2021 03:23
- Edited
0 votes 7 comments
Issues with LiftoverVcf Answered
- Mohammad Deen Hayatu
- October 06, 2022 06:43
0 votes 6 comments
SamToFastq - bam order Answered
- Jakub Savara
- July 24, 2022 10:48
0 votes 6 comments
GATK GenotypeGVCFs miss a real Insertion Answered
- touyupang
- February 18, 2022 07:45
0 votes 6 comments
How to evlauate the result: GenotypeConcordance or Concordance Answered
- lizhichao
- February 17, 2022 09:09
0 votes 6 comments
Theorical model for Active region detection Answered
- Naomie Abecassis
- June 22, 2021 14:26
0 votes 6 comments
STRANDQ missing from mutect2 vcf records Answered
- Rebecca Halperin
- May 12, 2021 19:26
0 votes 6 comments
GATK VariantEval no concordance between dbSNP and our data Answered
- Pierre_Bioinfo
- May 03, 2021 07:50
0 votes 6 comments
Calling somatic CNVs Answered
- Yasin Uzun
- September 09, 2020 02:34
0 votes 6 comments
use LearnReadOrientationModel to build artifact-prior.tar.gz Answered
- chenglei
- September 22, 2021 14:48
0 votes 5 comments

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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.