Documentation Questions

GATK GenotypeGVCFs miss a real Insertion Answered
- touyupang
- February 18, 2022 07:45
0 votes 6 comments
germline-resource Answered
- Juechen Yang
- March 17, 2020 17:32
0 votes 10 comments
Mosaic gCNVs with GATK Answered
- Naga
- January 13, 2022 17:32
- Edited
0 votes 1 comment
WDL pipeline: Mitochondrial-short-variant-discovery Answered
- manolis
- January 25, 2022 07:57
0 votes 2 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
stand_call_conf and stand_emit_conf in GATK 4.2.4.1 Answered
- M.R-E.H
- January 17, 2022 16:05
0 votes 1 comment
"main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit Answered
- 蒲鹏
- January 12, 2022 10:12
0 votes 4 comments
CollectReadCounts tutorial incorrectly states default read quality threshold Answered
- simon lee
- December 14, 2021 04:06
- Edited
0 votes 1 comment
Ploidy as an argument in Mutect2 Answered
- Michael Weinstein
- May 21, 2021 00:46
0 votes 5 comments
"NotDuplicateReadFilter" behaviour in HaplotypeCaller Answered
- sanjeevksh
- December 07, 2021 21:40
0 votes 3 comments
picard sortvcf: what does it do? Answered
- Thomas Juettemann
- November 09, 2021 17:31
0 votes 7 comments
Unable to find full Best Practices workflow for short variant joint genotyping
- Kirsten Dimmler
- November 23, 2021 17:41
0 votes 1 comment
What's wrong with my GATK HaplotypeCaller step's codes?
- Han Li
- November 29, 2021 05:18
0 votes 1 comment
Append GenomicsDBimport Answered
- wbsimey
- November 18, 2021 18:26
- Edited
0 votes 3 comments
How can I get Sample Summary
- rq m
- November 19, 2021 08:10
- Edited
0 votes 1 comment
GATK Best Practices Mitochondrial Analysis Answered
- ajwils
- January 09, 2020 21:15
- Edited
1 vote 45 comments
GATK4.2.3.0 HaplotypeCaller error
- Alicia
- November 13, 2021 12:49
0 votes 1 comment
BQSR: Do read filters used by BQSR tools need to be applied to data prior to assessing the number of bases per read group? Answered
- ISmolicz
- November 17, 2020 17:02
0 votes 2 comments
FilterFuncotations Duplicate key error Answered
- Azza Ahmed
- October 14, 2021 10:53
0 votes 7 comments
Where do I find guidance on when to mark duplicates a second time? Answered
- ISmolicz
- November 13, 2020 11:54
1 vote 2 comments
--dbsnp option in HaplotypeCaller and other programs Answered
- gwotto
- July 01, 2021 12:21
0 votes 3 comments
haplotypeCaller phasing Answered
- Jeremie Kalfon
- October 05, 2021 15:07
- Edited
0 votes 11 comments
`FilterMutectCalls` for normal only calls Answered
- AMN
- September 10, 2021 16:17
- Edited
0 votes 4 comments
How does Genomicsdbimport for polyploids work?
- Homa Papoli
- October 25, 2021 08:57
0 votes 2 comments
VariantsToTable GT not extracting correctly Answered
- Asha Mehta
- October 15, 2021 19:59
- Edited
0 votes 1 comment
Difference between the different annotation groups available in GATK
- Shashank Nagaraja
- October 04, 2021 22:15
2 votes 1 comment
GATK VariantFiltration Error Answered
- Reza
- September 05, 2021 07:48
0 votes 3 comments
use LearnReadOrientationModel to build artifact-prior.tar.gz Answered
- chenglei
- September 22, 2021 14:48
0 votes 5 comments
How do I call somatic mitochondrial variants? Answered
- Ruiqiao Bai
- September 14, 2021 04:03
0 votes 3 comments
Interpretation of gene_summary output from DepthofCoverage Answered
- neethukrishna Kausthubham
- August 26, 2021 11:08
0 votes 11 comments

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