I am working on joint genotype call of gvcf files of 200 samples. This is my first time with vcf data. I get the format. but I am struggling with some basic questions like
What is a reference allele e.g. in hg19 file from 1000 genomes_phase3? Is it the reference allele seen on most of people sequence?
What is an alternate allele? Is it the one which is minor allele at that variant and position?
What is NON_REF allele in alt. allele column?