e-learning
Calling very rare variants
Abstract
This page explains how to perform discovery of low frequency variants from duplex sequencing data. As an example we use the ABL1 dataset published by Schmitt and colleagues (SRA accession SRR1799908).
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- What frequency of variants is so low that it is obscured by sequencing error rate?
- What are the different types of consensus sequences produced from duplex sequencing?
Learning Objectives
- Processing raw duplex sequencing data into consensus sequences
- Find rare variants without relying on diploid assumptions
Licence: Creative Commons Attribution 4.0 International
Keywords: Variant Analysis
Target audience: Students
Resource type: e-learning
Version: 20
Status: Draft
Prerequisites:
- Introduction to Galaxy Analyses
- Mapping
- Quality Control
Learning objectives:
- Processing raw duplex sequencing data into consensus sequences
- Find rare variants without relying on diploid assumptions
Date modified: 2023-11-09
Date published: 2017-02-22
Contributors: Anton Nekrutenko, Nick Stoler
Scientific topics: Genetic variation
External resources:
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