mutation vs snp

Question

[fatimarasool135]

Hi. I have found the snps by samtools. I want to know the biological significance or annotation of these snps.? how can i found these snps are involved in any disease ?

Answer 1

[h.mon]

Use VEP, Annovar, snpEff, ...

You should provide more details, like which organism (human?), did you perform mapping or de novo assembly, which filters did you apply, and so on.

[fatimarasool135]

Mapping with reference genome

Answer 2

[finswimmer]

This is a very general question. More details about your aim would be helpful.

This is why I gave you a more general answer: Use VEP from ensembl. If you have an (rs)ID you can also search directly for it on ensembl. For each variant you can find a "phenotype data" page if data are available, e.g. rs699.

fin swimmer

[fatimarasool135]

i have excel file...in which i have only chromosome number,position of snp ,etc...this excel file not contain any id or genes in which thess snps are known. i want to know the corresponding genes and proteins of snps

[finswimmer]

Than VEP is really the place you should go.