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lets review what a vcf file is vcf stands for variant call format and as opposed to a fasta or bam file which store long genomic sequences vcf files store variants only to understand better lets take a look at the vcf file well be loading into igv so here it is this is the top of our vcf file as we scroll down were going to see the three parts that make up a vcf the meta information the header and the variance what we see here are rows of meta information which always start with a double hash more importantly we see the version of the vcf format and the reference genome that was used to call the variants in this file lets scroll down through the rest of the meta information until we come to the header believe it or not this is one line of data its just so long that it needs to be wrapped onto multiple lines each item in the header is a column in the vcf these first eight columns are required in bcf files and define the variant site they are the chromosome the variant is on its p
