How to retrieve SNP numbers from the VCF then find information about them whether they are intron on exon variant ?

Question

[mohammedabeddin1]

I have a VCF file for SCN9A gene which has multiple SNP's in it. I want to retrieve those SNP numbers from the file and also find the relevant information about them whether they are intron variant or exon variant.

Answer 1

[rbagnall]

There are lots of 'variant annotation' posts on Biostars. I would annotate the vcf first, then retrieve the SNPs you want. There are simple online tools for this:

SeattleSeqAnnotation will do the job.
Ensembl VEP will do the job.