How to distinguish INDELs from SNPs.

Question

[elb]

Hi guys, how small insertions (INDELS of 1bp) are distinguished from SNPs? Is there a catalogue for SNPs?

Thank you in advance

[Giovanni M Dall'Olio]

What type of data are you looking at? Do you have a dataset of WES data and you want to call SNPs, or do you simply want to explore existing annotations?

[elb]

Hi, data are WGS. I just would like to know based on what the 1bp substitution found by the variant caller is classified as SNP or small INDEL with possible functional consequence? I'm totally new to the field.

Answer 1

[colindaven]

Please have a look at this nice image summarizing SNPs and INDELs ...

https://www.rna-seqblog.com/grom-lightning-fast-genome-variant-detection/

Your question isn't clear, but maybe check out Ensembl VEP for predicting effects of indels and SNPs on protein function.

Answer 2

[Jorge Amigo]

I would recommend reading about basic biology and genetic variants before even starting looking into WGS files:

https://bitesizebio.com/23996/whats-so-important-about-variants/

https://www.ebi.ac.uk/training/online/courses/human-genetic-variation-introduction/what-is-genetic-variation/types-of-genetic-variation/

https://medlineplus.gov/genetics/understanding/mutationsanddisorders/possiblemutations/

...

and then I would read about VCF format, as I'm almost certain that you'll end up dealing with them.

Regarding "a" SNP catalogue, if you need a single reference I would go for dbSNP.