Understanding File Formats in Bioinformatics - VCF and gVCF

Explore the intricacies of Variant Call Format (VCF) and genomic VCF (gVCF) files in this comprehensive 26-minute video tutorial. Delve into the structure and organization of VCF files, examining various fields and their significance in variant calling analysis. Learn about metadata sections, header lines, and data lines while understanding how genetic information is stored. Discover the concepts of genotypes, phased and unphased genotypes, and how to calculate alternate allele frequencies. Gain insights into recording DNA variations and interpreting VCF records. Finally, explore the differences between VCF and gVCF files, enhancing your understanding of file formats crucial for bioinformatics research and analysis.

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