Variant Analysis — Editorial Board Home

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Editorial Board

orcid logoWolfgang Maier avatar Wolfgang Maierorcid logoBérénice Batut avatar Bérénice BatutAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBjörn Grüning avatar Björn Grüning

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Topic Materials

Material Contributions v2 Pre-requisites Follow up trainings Data on Zenodo Notebook Server Compatibility
Introduction to Variant analysis ❌ ❌ ❌ ✅ ❌
Calling variants in diploid systems ❌ ❌ ❌ ✅ ❌
Calling variants in non-diploid systems ❌ ❌ ❌ ✅ ❌
Calling very rare variants ❌ ❌ ❌ ✅ ❌
Microbial Variant Calling ❌ ❌ ❌ ✅ ❌
Mapping and molecular identification of phenotype-causing mutations ❌ ❌ ❌ ✅ ❌
Avian influenza viral strain analysis from gene segment sequencing data ❌ ❌ ❌ ✅ ❌
From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis ✅ ❌ ❌ ✅ ❌
M. tuberculosis Variant Analysis ❌ ❌ ❌ ✅ ❌
Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data ✅ ✅ ❌ ✅ ❌
Pox virus genome analysis from tiled-amplicon sequencing data ✅ ✅ ❌ ✅ ❌
Exome sequencing data analysis for diagnosing a genetic disease ❌ ❌ ❌ ✅ ❌
Identification of somatic and germline variants from tumor and normal sample pairs ❌ ❌ ❌ ✅ ❌
Somatic Variant Discovery from WES Data Using Control-FREEC ❌ ❌ ❌ ✅ ❌
Trio Analysis using Synthetic Datasets from RD-Connect GPAP ❌ ❌ ❌ ✅ ❌
Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs) ❌ ❌ ✅ ✅ ❌
Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons ❌ ✅ ❌ ✅ ❌

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
Calling variants in diploid systems Diploid Dec 23, 2024 3 ❌ ❌ ❌
Calling variants in non-diploid systems Calling variants in non-diploid systems Dec 23, 2024 2 ✅ ❌ ❌
Calling very rare variants Du Novo GTN Tutorial - Make Consensus Sequences Dec 23, 2024 3 ❌ ❌ ❌
Calling very rare variants Du Novo GTN Tutorial - Variant Calling Dec 23, 2024 3 ❌ ❌ ❌
Microbial Variant Calling Microbial Variant Calling Dec 23, 2024 4 ✅ ❌ ❌
Mapping and molecular identification of phenotype-causing mutations Mapping And Molecular Identification Of Phenotype Causing Mutations Dec 23, 2024 3 ❌ ❌ ❌
From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis Simple COVID-19 - PE Variation Dec 23, 2024 1 ❌ ❌ ❌
M. tuberculosis Variant Analysis TB Variant Analysis v1.0 Dec 23, 2024 7 ✅ ✅ ❌
Pox virus genome analysis from tiled-amplicon sequencing data pox-virus-tiled-amplicon-ref-masking Dec 23, 2024 2 ✅ ❌ ❌
Exome sequencing data analysis for diagnosing a genetic disease Exome Seq Training Pre-Mapped W Cached Ref Dec 23, 2024 5 ✅ ❌ ❌
Exome sequencing data analysis for diagnosing a genetic disease Exome Seq Training Full W Cached Ref Dec 23, 2024 5 ✅ ❌ ❌
Identification of somatic and germline variants from tumor and normal sample pairs Identification of somatic and germline variants from tumor and normal sample pairs tutorial Dec 23, 2024 1 ✅ ❌ ❌
Somatic Variant Discovery from WES Data Using Control-FREEC Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC Dec 23, 2024 1 ✅ ❌ ❌
Trio Analysis using Synthetic Datasets from RD-Connect GPAP Trio Analysis Tutorial Dec 23, 2024 5 ✅ ❌ ❌

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