Biostar Beta. Not for public use.
any database for 1000G MAF available?
1
Entering edit mode
21 months ago
J.F.Jiang • 750
China

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&gts=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,

MAF SNP 1000G • 2.0k views
ADD COMMENTlink
2
Entering edit mode
12 months ago
Leandro Lima • 920
San Francisco, CA

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
0
Entering edit mode

Hi Leandro,

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

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1