Understanding SNP variant output

Question

[Ada]

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT

What does the REF and ALT refer to in extraction of variants?

[Pierre Lindenbaum]

see https://samtools.github.io/hts-specs/VCFv4.2.pdf

Answer 1

[reza.jabal]

In re-sequencing applications such as Whole-exome/Genome sequencing (WES/WGS), we align the sequenced contigs against a reference genome which is perceived as ground truth for the correct letter at each position. The REF represents the reference allele, and ALT represent anything else that is not a reference allele (also called alternative!). These two terms are occasionally confused with Major and Minor allele that rather have population connotation.

To familiarize yourself with the file format you are showing I recommend reading the Variant Call Format (VCF) specifications.