In the variant call format v4.1,one example showed the variant result as follows:
ref:G, alt: A, NA00001:0|0,NA00002:1|0,NA00003:1/1.
Every snp position of variants is like above. I was very confused. Is not there any snp position which changed to any other genotype like C,T? At this position, we had many samples, but i could not find any other alterations like the substance i mentioned above.
Short answer: No, you won't see non REF ALT nucleotides at that position in any of your samples.
Long answer: VCF stores entries like so:
Each line is a position in the ref genome that sees a difference in at least one of your samples. If a sample has REF/REF, you'd see 0/0. ALT/ALT is 1/1. REF/ALT is 0/1 - these are the genotypes (homozygous and heterozygous).
Multi allelic variants are where multiple (>2) bases are seen at the same locus on the samples. Multi allelic variants usually have a comma separated list of ALT alleles.
So, if you see only 1 REF and 1 ALT allele, you can rest assured that all your samples either contain REF/REF, ALT/ALT or REF/ALT. No third nucleotide is involved at that position.