Variant Analysis

Welcome to the Variant Analysis track. Here you can learn about Variant Analysis. If you need support during the event contact us via the Slack Channel.

Organiser(s) orcid logoKrzysztof Poterlowicz avatar Krzysztof Poterlowiczorcid logoKhaled Jum'ah avatar Khaled Jum'ah
Instructor(s) orcid logoAnna Syme avatar Anna Symeorcid logoKhaled Jum'ah avatar Khaled Jum'ahorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoKatarzyna Kamieniecka avatar Katarzyna KamienieckaMingkai Wang avatar Mingkai Wang

Variant Analysis introduction

If you are new to Variant Analysis, please start with the following tutorials. They cover the essential knowledge about Variant Calling in different diploid systems and organisms. If you encounter any issues, please ask us on Slack.

Lesson Slides Hands-on Recordings
Calling variants in diploid systems
Calling variants in non-diploid systems
prokaryote microgalaxy
Calling very rare variants
Microbial Variant Calling
prokaryote microgalaxy gmod jbrowse1

Advanced analysis

Here are some more advanced tutorials you can follow if you like. They apply the previous knowledge to selected use cases and introduce Beacon for data sharing and queries. If you encounter any issues, please ask us on Slack.

Lesson Slides Hands-on Recordings
Identification of somatic and germline variants from tumor and normal sample pairs
Somatic Variant Discovery from WES Data Using Control-FREEC
Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
covid19 virology one-health
Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons
Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs)