This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to find refgene location for SNPs?

I have some SNPs that I need to find refgene location (non-synonymous, ncRNA_exonic,splicing, etc) given the chr: position:REF:ALT. I have tried VEP tool, but that does not give me what I want.

I have these SNPs:

chr15:72105885:G:A # and I want: nonsynonymous SNV
chr16:1115931:C:G # and I want: ncRNA_exonic
snps refgene
• 3,321 views • link
updated by Ram Ram • written by MAPK MAPK

1 answer

ANNOVAR Package.

If your input file is input.vcf, the output file input.vcf.variant_function will have this information for each variant.

• 0 views • link
updated by Ram Ram • written by venu venu

The SNPs I have were already passed through annovar and have "unknow" location for those SNPs. What does "unknown" mean? Is there anything else I can use to get refgene location (I don't want to use ensemble)?

• 0 views • link
written by MAPK MAPK

In the provided link, go down and find rule 4

If a transcript maps to multiple locations, all as "coding transcripts", but none has a complete ORF, then this transcript will not be used in exonic_variant_function annotation and the corresponding annotation will be marked as "UNKNOWN".

• 0 views • link
updated by Ram Ram • written by venu venu

Thanks Venu. Another question I have is some of the SNPs are labelled as Unknown by annovar, but ensemble has identified as nonsynonymous SNV. What is difference between these two?

• 0 views • link
written by MAPK MAPK

Hi, sorry to interrupt your both conversation. I'd like to ask an almost similar question. All of my variants that undergo the WES, was completely annotated in Annovar. however, some of the variants were denoted as a dot (.) and "Unknown" for the Exonic Function RefGene and Exonic FunctionKnownGene, while the other variants were annotated as frameshift, synonymous etc.

so, what does that mean for both dot (.) and "Unknown"? thanks in advance!

• 0 views • link
written by nuratikah_norazhar • nuratikah_norazhar

Log in to answer this question.

More posts like this