Question: How to annotate novel SNPs using coding sequence position?
0
gravatar for bioinfo89
2.2 years ago by
bioinfo8940
bioinfo8940 wrote:

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.

snp • 752 views
ADD COMMENTlink modified 2.2 years ago by Emily_Ensembl19k • written 2.2 years ago by bioinfo8940
1
gravatar for Emily_Ensembl
2.2 years ago by
Emily_Ensembl19k
EMBL-EBI
Emily_Ensembl19k wrote:

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

ADD COMMENTlink written 2.2 years ago by Emily_Ensembl19k

Yes, Thank you, it worked.

ADD REPLYlink written 2.2 years ago by bioinfo8940
0
gravatar for colindaven
2.2 years ago by
colindaven1.7k
Hannover Medical School
colindaven1.7k wrote:

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.

ADD COMMENTlink written 2.2 years ago by colindaven1.7k
0
gravatar for bioinfo89
2.2 years ago by
bioinfo8940
bioinfo8940 wrote:

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!

ADD COMMENTlink written 2.2 years ago by bioinfo8940

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.

ADD REPLYlink written 2.2 years ago by colindaven1.7k
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