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How can get MAF for set of SNPs from each population based on 1000 Genome?
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13 months ago
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Netherlands

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.

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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.

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

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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

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