NEWBIE: What is relation between SNP calling, INDEL calling and Genotype calling?

[arkilis]

I know the snp is replace polymorphism and INDEL is about deletion or insertion. Are they relative to genotype calling, any stories? thx

[sBeier]

A polymorphism is more general than a SNP. A SNP is a single nucleotide that is different. (Single Nucleotide Polymorphism). About the Indels, you already got it right.

The genotype is the complete genetic makeup of an organism. So, in a way it is related to SNPs and Indels. If you compare different organisms from the same species (or strain/subspecies, as far down as you get), even if they are closely related their genotype will differ, especially through SNPs and Indels. There might also be bigger differences, even up to chromosomal mutations, but those two are the most frequent.

[mikep]

A diploid organism contains two copies of each chromosome. If there is a SNP at a particular position then there are 3 possibilties
both chromosomes contain the SNP (homozygous for the SNP)
one chromosome contains the SNP and the other the WT sequence (heterozygous)
neither contain the SNP (homozygous for the WT)

the SNP's on one chromosome are described as a haplotype. put two chromosomes together and you have a genotype. If you sequence multiple individuals, then you can also work out the genotype frequency, such as how many people are heterozygous for a SNP, or the MAF (minor allele frequency, what % of people carry the SNP).

[swbarnes2]

Stories?

In general, genotyping is when you know exactly which variant you want to look at, and likely you have an assay that will give you exactly that information, and no more. With something like Illumina sequencing, you get a lot more than just one site, so it's not really genotyping.

Also, it's probably better to get in the habit of calling them SNVs; small nucleotide variants. "Single" is obviously kind of limiting" and "polymorphism" suggests that the variant is common in a population, which not all variants are.

[arkilis]

Thanks all!

Here is some conclusion of the above discussions:

SNP calling/detection aims to determine in which positions there are polymorphisms, or in which positions at least one of the bases differs from a reference sequence. The latter is also sometimes referred to as 'variant calling'.

INDEL is another polymorphism that more about deletion or insertion.

Genotype is genetics expression related with SNPs and INDELs. There might also be other bigger factors, even up to chromosomal mutations, but those two are the most frequent. the SNP's on one chromosome are described as a haplotype. put two chromosomes together and you have a genotype. If you sequence multiple individuals, then you can also work out the genotype frequency, such as how many people are heterozygous for a SNP, or the MAF (minor allele frequency, what % of people carry the SNP). (From @sBeier and @mikep)