Whats the Difference between variants and SNPs in IGV?(or in general)

Question

[tmrhyd]

I have a VCF file and a Bam file in IGV and am trying to find out what variants are have the loudest signal by lining up the variant mark given by the VCF track to the colored base line in the .bam coverage track. Does this sound like it is the right way to tell if something is the best SNP/Variant?

So sorry if this is confusing, I'm confused too.

Thank you!!

Answer 1

[Ram]

There are quite a few terms used to describe nucleotide changes between a reference sequence and a different sequence. SNV, SNP, variant, mutation, polymorphism, etc are widely used, and the specific meanings they bear are often localized to a team or an institution. Even dbSNP does not store just SNPs.

The broadest of these single nucleotide terms is Single Nucleotide Variation/Variant, which simply means "one nucleotide has changed". Polymorphisms mostly refer to such changes that occur frequently in a population and as such are mostly benign, thus assuming "different forms". Mutations refer to more damaging changes, because "mutation" sounds more sinister, I guess.

As long as you define what you mean by the word, you'll be fine, but here's a general usage guideline: variant = neutral, polymorphism = not bad, mutation = probably bad.