Question: How can get MAF for set of SNPs from each population based on 1000 Genome?
0
gravatar for star
2.8 years ago by
star70
Netherlands
star70 wrote:

I have a set of SNPs (500 SNPs), I would like to get MAF (minor allele frequency) for them besed on 1000 Genome for each population (Europe, Africa , America, and ...).

I can find them by searching each SNPs separately and also using BioMart but I would like to get for each population.

If there is a way for finding it preferably using R, please help me.

ensembl 1000 genome ucsc R hapmap • 1.3k views
ADD COMMENTlink modified 11 weeks ago by zx87546.0k • written 2.8 years ago by star70
1

hi, I have not used R/BioC package, but if you go to the UCSC Table Browser, then the 1000G data (1000g phase 3 vars track) looks like this - http://s11.postimg.org/6n8fe7m37/Screen_Shot_2016_03_09_at_13_55_36.png

Since your list is just 500, you could easily use Table Brwsr utility to get the data and then basically parse the allele freq. in the Info col.

ADD REPLYlink modified 11 weeks ago by Kevin Blighe33k • written 2.8 years ago by Amitm1.6k

Thanks a lot for your help, But would you please help me how can I put 1000G as track.

ADD REPLYlink written 2.8 years ago by star70
1

See thsi setting,

And you could use identifiers to provide your SNP list.

http://s17.postimg.org/6ob298evz/Screen_Shot_2016_03_09_at_14_21_40.png

ADD REPLYlink modified 11 weeks ago by Kevin Blighe33k • written 2.8 years ago by Amitm1.6k
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