Question: How to retrieve SNP numbers from the VCF then find information about them whether they are intron on exon variant ?
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gravatar for mohammedabeddin1
4.7 years ago by
mohammedabeddin110 wrote:

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.

snp • 1.0k views
ADD COMMENTlink modified 4.7 years ago by rbagnall1.7k • written 4.7 years ago by mohammedabeddin110
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gravatar for rbagnall
4.7 years ago by
rbagnall1.7k
Australia
rbagnall1.7k wrote:

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.

ADD COMMENTlink written 4.7 years ago by rbagnall1.7k
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