Question: any database for 1000G MAF available?
1
gravatar for J.F.Jiang
4.7 years ago by
J.F.Jiang750
China
J.F.Jiang750 wrote:

Hi all,

As a useful tool, the NCBI website offers us great resource to discover the information, e.g. SNPs.

For example, this website: http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/?chr=NC_000010.10&from=60023&to=61023&mk=60523:60523|rs148087467>s=rs187110906, can provide all infromation, MAF from 1000G datasets for all populations.

I can download the raw vcf files from the ftp, and using vcftools or plink to calculate all the required MAFs for all population, however, is there any public data that can be downloaded?

If anyone knows, plz let me know.

Best,

 

snp 1000g maf • 1.9k views
ADD COMMENTlink modified 4.7 years ago by Leandro Lima920 • written 4.7 years ago by J.F.Jiang750
2
gravatar for Leandro Lima
4.7 years ago by
Leandro Lima920
San Francisco, CA
Leandro Lima920 wrote:

Hi J.F.Jiang.

You can download the vcf files here:

ftp://ftp.ensembl.org/pub/release-76/variation/vcf/homo_sapiens/

your use Ensembl Biomart API to get the information using web or R:

For example, using R:

# To install biomaRt
# source("http://bioconductor.org/biocLite.R")
# biocLite("biomaRt")


library(biomaRt)

snpsMart = useMart("snp", dataset = "hsapiens_snp")

# listAttributes(snpsMart)
snps_attributes = c('refsnp_id', 'chr_name', 'chrom_start', 'minor_allele_freq')

# listFilters(snpsMart)
snps_filters = c('snp_filter')

snps_values = c('rs185293715', 'rs61838549', 'rs28782254') # for example

snps_results = getBM(attributes = snps_attributes, filters = snps_filters, values = snps_values, mart = snpsMart)

 

ADD COMMENTlink written 4.7 years ago by Leandro Lima920

Hi Leandro Lima

Thanks for your reply,

I have checked the ensemble variation vcf file before and found that it only provides global MAF based on some larger population sets, AFR, ASN, AMR, EUR, which is the same as the resource data of ANNOVAR. My idea is to obtain some more specific population category, such as CHB CHS CEU ...;

The sencond R portal, however, did not provide specific population information for MAF, but providing the global MAF based on all 1000G samples.

I have downloaded the 1000G vcf files and calculated with plink to obtain the MAFs though it is time consuming.

Thanks!

ADD REPLYlink written 4.7 years ago by J.F.Jiang750
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