Question: Api Or Ui For 1000 Genomes Sample Genotypes
3
gravatar for win
6.7 years ago by
win860
India
win860 wrote:

hi all. i have a list of rs# and other variants that only have chromosome number and variation position (hg19). for each of the variants i want genotypes of all samples in 1000Genomes.

i want to know if there is an API or an UI can allow for this?

thanks.

1000genomes • 1.9k views
ADD COMMENTlink modified 6.7 years ago by Pierre Lindenbaum131k • written 6.7 years ago by win860
3
gravatar for rbagnall
6.7 years ago by
rbagnall1.7k
Australia
rbagnall1.7k wrote:

If you only have a few variants, and want a UI...

go to the 1000 genomes browser, e.g.

http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/?chr=NC_000011.9&from=47354287&to=47355287&mk=47354787:47354787|rs1052373>s=rs1052373

from here you can enter a position (chr11:47354287) on the left hand side, below the idiograms. Then 'download data for this region' (right hand side, just above the genotypes) retrieves the genotypes of the 1000Genomes samples as a VCF file (right hand side, just above the genotypes).

ADD COMMENTlink written 6.7 years ago by rbagnall1.7k

this is probably close but not exactly what i need. i have about 1500 variants and the UI allows for only one search at a time.

ADD REPLYlink written 6.7 years ago by win860
1
gravatar for Pierre Lindenbaum
6.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

(not tested)

get the positions of your rs## and put them into a BED file.

Then call tabix for each chrom :

tabix -h -B ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz your.bed
ADD COMMENTlink written 6.7 years ago by Pierre Lindenbaum131k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1983 users visited in the last hour