hands-on tutorial

Explore and filter variants in your browser

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A 15-minute hands-on tutorial: summarise a VCF with bcftools stats, filter variants by quality and depth, and extract a table with bcftools query, all in the browser with nothing to install.

Licence: Creative Commons Attribution 4.0 International

Keywords: VCF, bcftools, genetic variants, variant filtering, workflow

Competency level: • Beginner

Resource type: hands-on tutorial

Learning objectives:

  • Extract chosen fields into a table with bcftools query
  • Filter variants by quality and read depth
  • Mark weak variants instead of removing them
  • Summarise a VCF file with bcftools stats

Authors: IEETA, University of Aveiro

External resources:
BioChef
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