How to get a unique target gene for each SNP from different chromosomes/genes in a list at once?

Question

[cmcouto.silva]

Hello, folks!

I have a huge list with SNPs from different chromosomes/genes (human data set), and I wanna know the target genes for each one of them at once (if possible). It would be important to catch only one gene ID per SNP (top rated).

---

I have tried using the Ensembl Biomart Tool setting the following parameters:

Data set: Human Short Variants (SNPs and indels excluding flagged variants) (GRCh38.p10)

Filters:

• Chromosome/scaffold: Chromosomes that I know to have those SNPs
• Filter by Variant name (e.g. rs123, CM000001) [Max 500 advised]: SNP list (rs*)

Attributes

• Chromosome/scaffold name
• Variant name
• Gene stable ID

Nevertheless, I got an even bigger list with repeated SNPs and Ensembl ID's for the target genes when I expected unique and usual gene symbol. For example, I would expect "TP53" for "rs1042522", "LAMB3" for "rs80356682", and so on...

Any help/tip would be greatly appreciated!

[cpad0112]

bedtools intersect ?

Answer 1

[Maxime Lamontagne]

Try ANNOVAR table_annovar.pl) : http://annovar.openbioinformatics.org/en/latest/user-guide/startup/

Answer 2

[Alex Reynolds]

You could use BEDOPS bedmap to map positions from vcf2bed to gene names from gff2bed:

$ bedmap --echo --echo-map-id-uniq <(vcf2bed < snps.vcf) <(gff2bed < genes.gff) > answer.bed

This gives you SNP positions and their metadata, along with a list of overlapping gene IDs.