Api Or Ui For 1000 Genomes Sample Genotypes

Question

[win]

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.

Answer 1

[rbagnall]

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).

[win]

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.

Answer 2

[Pierre Lindenbaum]

(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