Overview
This course covers the learning outcomes and goals of understanding file formats in bioinformatics, specifically focusing on VCF and gVCF files. The course teaches the organization and information stored in VCF files, including fields, genotypes, allele frequencies, and DNA variations. It also explains the differences between phased and unphased genotypes, as well as the specifics of genomic VCF files. The teaching method involves a 26-minute video lecture with examples and explanations. The intended audience for this course includes bioinformatics professionals, researchers, and students looking to enhance their understanding of variant calling analysis and file formats in genomics.
Syllabus
Intro
What is a VCF file and how is it generated?
Main sections of a VCF file
Metadata section
Header line
Data lines - description of fields
Genes and alleles
Understanding genotype
What does genotype 2/0 or 1/2 mean?
Difference between GT:0/1 and GT:0|1 - phased vs unphased genotype
How are variants recorded in a VCF file?
Interpreting a record in VCF
Genomic VCF gVCF
Taught by
bioinformagician
Reviews
5.0 rating, based on 1 Class Central review
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Excellent and easy-to-follow explanation. Anyone working on genomics data must know the details in the VCF/GVCF files and what information they carry. I will recommend this tutorial to any beginner working with VCF files.