Question: How can I get a list of all SNPs from a gene of my interest?
1
gravatar for Mahantesh Biradar
3.4 years ago by
Taipei, Taiwan
Mahantesh Biradar30 wrote:

I would like to download the list all SNPs for a gene of my interest with all their details like Chromosome, Physical position etc. How can I do this?

snp hapmap ncbi gene • 2.2k views
ADD COMMENTlink modified 3.4 years ago by Ibrahim Tanyalcin980 • written 3.4 years ago by Mahantesh Biradar30
1

A: How do I ask a question on Biostars?

Search first - Make sure the question on your mind hasn't been answered already. Search on biostars AND on google.

ADD REPLYlink written 3.4 years ago by Pierre Lindenbaum122k
5
gravatar for Ibrahim Tanyalcin
3.4 years ago by
Belgium
Ibrahim Tanyalcin980 wrote:

Dear Mahantesh,

For people who are not used to command line, biomart has a very nice interface for downloading SNPs etc. Go to http://www.ensembl.org/biomart/martview/ . You can filter based on gene IDs, you will find these on ensembl/UCSC.

ADD COMMENTlink written 3.4 years ago by Ibrahim Tanyalcin980

Thank you Ibrahim. I had a question; I followed your response and got a table. Why some refSNPs are listed more than once? Is that because of alternative splicing or I have done something wrong? Variant name Protein location (aa) Variant alleles

rs141402957------------------T/C

rs28934578-------175-------C/A/T

rs141402957----- 312-------T/C

rs28934578------- 136-------C/A/T

rs28934578------- 43---------C/A/T

rs141402957----- 219-------T/C

rs141402957-----192--------T/C

rs28934578-------16---------C/A/T

rs141402957------351-------T/C

rs28934578--------82--------C/A/T

rs28934578-------------------C/A/T

rs141402957-----340-------T/C

rs28934578-------164-------C/A/T

ADD REPLYlink modified 3 months ago • written 3 months ago by english.server160

Hi there, sorry for the delay. I think I had a script that filters duplicates (https://github.com/IbrahimTanyalcin/I-PV/blob/master/ipv/script/invokeCircos.pl), though it is used for visualization. You can do the same with python/perl or whatever you fancy.

ADD REPLYlink written 3 months ago by Ibrahim Tanyalcin980
1
gravatar for Alex Reynolds
3.4 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

Get all SNP rs* IDs via the command line:

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N -e 'SELECT chrom, chromStart, chromEnd, name FROM snp142Common' hg19 > snp142Common.bed

Get genes and convert to BED with gtf2bed:

$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz \
    | gunzip -c \
    | grep -w "gene" \
    | gtf2bed \
    > genes.bed

Adjust this step for whichever annotations you use or prefer.

Filter gene names for the gene of interest, then map SNPs to gene, using bedmap to look for SNPs whose positions overlap those of Gencode genes:

$ grep -w 'name-of-gene' genes.bed | bedmap --echo snp142Common.bed - > answer.bed
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Alex Reynolds28k

Can you possibly give a real example? I dont know linux and dont know what is the order of commands and for example how to enter 'SELECT chrom, chromStart, chromEnd, name FROM snp142Common'

ADD REPLYlink modified 3 months ago • written 3 months ago by english.server160
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