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 42 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
VCF allelic depth (AD) supports the reference or alternate?
- Nikki Lukasko
- February 15, 2024 23:44
0 votes 13 comments
How to use the --alleles option of HaplotypeCaller ?
- Chloé Girard
- November 10, 2023 16:58
- Edited
0 votes 13 comments
Germline sites in Mutect2 Answered
- G E
- March 19, 2021 04:39
- Edited
0 votes 13 comments
GenotypeGVCFs only accepts single combinedGVCF? CombineGVCFs & genomicsdb errors... .interval_list subset Answered
- Mingzhou Fu
- July 29, 2021 22:42
0 votes 12 comments
GenomAD files for MuTect2 Answered
- Felix
- May 06, 2020 10:18
0 votes 12 comments
How does Mutect2 count read depth/coverage? Answered
- Sameer Shankar
- February 16, 2023 20:40
2 votes 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
CreateSomaticPanelOfNormals BETA tag Answered
- G E
- April 01, 2021 19:38
0 votes 11 comments
germline-resource Answered
- Juechen Yang
- March 17, 2020 17:32
0 votes 10 comments
GenotypeGVCFs generates an empty VCF file with all my samples
- Laura Rey Vargas
- March 18, 2024 14:34
0 votes 9 comments
Error while creating conda environment using gatkcondaenv.yml
- saurabh
- April 04, 2024 13:24
0 votes 8 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
Where is the list of annotations and annotation groups? Answered
- tedtoal
- July 05, 2021 23:05
2 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
Genotype filtering still write "PASS" in filter field
- Marissa Eronika
- March 21, 2023 15:50
1 vote 7 comments
Issues with LiftoverVcf Answered
- Mohammad Deen Hayatu
- October 06, 2022 06:43
0 votes 7 comments
Documentation for running GATK and Cromwell on IBM Cloud Answered
- Takeshi Yoshimura
- April 05, 2022 01:24
1 vote 7 comments
Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. Answered
- tahi
- February 22, 2022 08:48
0 votes 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
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
How do adapter sequences not contribute to alignment if the base quality is set to 2 with SamToFastq but BWA-MEM does not consider base quality scores? Answered
- ISmolicz
- April 07, 2021 14:37
- Edited
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

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