candidate gene identification

Question

[dinesh]

Hi community, need suggestions

I have physical position of SNPs and I have to find the candidate gene near by SNPs. help to solve this problem.

e.g.:

chromosome 3 position  196643035

Answer 1

[Alex Reynolds]

Convert your SNP positions to sorted BED3 format with awk or similar, to make a file called snps.bed.

Download annotations and convert to BED. For example:

$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_21/gencode.v21.annotation.gff3.gz \
    | gunzip --stdout - \
    | awk '$3 == "gene"' \
    | convert2bed -i gff - \
    > genes.bed

Then use closest-features to find the nearest annotation to each SNP:

$ closest-features snps.bed genes.bed > answer.bed

Answer 2

[Ram]

Use the UCSC genome browser. Explore it, and you can visualize multiple factors in context.

In other news, you really need to learn how to phrase your questions well.