Understanding VCF file | Variant Call Format Part 1/3
Variant Call Format is a text file that contains information of the "Variants" between the references genome and the sample genome. It contains meta-information lines, a header line, and then data lines each containing information about a position in the genome. The format also has the ability to contain genotype information on samples for each position
It was used extensively during the 1000 human genome projects for GWAS analysis and was included in many bioinformatics research pipeline. Yet, most researchers are having problems understanding how this file can be read directly and be used in their analysis.
In this 3 part videos, I am going to go through the whole specification of the .vcf file format. The metadata section, data section, and some examples to check if your understanding matches mine.
Link to slides
http://bit.ly/Brandon_Yeo
Original specification file
https://samtools.github.io/hts-specs/...
Sample vcf
https://drive.google.com/file/d/1EhAn...
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