How to annotate novel SNPs using coding sequence position?

Question

[bioinfo89]

Hello!

I have a list of novel mutations with coding sequence positions (not in vcf format). I want to annotate them to know how many of them are deleterious.

As per my knowledge we require the genomic positions to use in for annotation in ANNOVAR (creating a vcf file or annovar format), however since I have coding sequence positions I am not sure how to proceed.

Any suggestions how to do it?

Thank you in advance.

Answer 1

[Emily]

Are they in HGVS? You can use that as input for the VEP.

[bioinfo89]

Yes, Thank you, it worked.

Answer 2

[colindaven]

I would recall your SNPs in a standard format - VCF. Then use Annovar, Ensembl VEP or snpEff to call. Otherwise you're going to have to script it with biopython or similar. That's going to be a world of pain considering it's essentially a solved problem.

Answer 3

[bioinfo89]

Hi colindaven,

I have a novel mutation list complied from literature review, so I cannot recall the SNPs. I wanted to know if I could use these mutation list with coding sequence positions (since genomic position was not available) to annotate.

Thanks!

[colindaven]

Sounds like you'll have to convert to a standard format. Try a minimal VCF version, it's probably easiest and best documented (in my experience). You probably don't need the INFO or GT columns. Good luck.