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

1

Entering edit mode

8.1 years ago

star ▴ 350

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.

R 1000 Genome hapmap ucsc Ensembl • 3.3k views

ADD COMMENT • link updated 5.6 years ago by zx8754 11k • written 8.1 years ago by star ▴ 350

1

Entering edit mode

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 REPLY • link updated 5.6 years ago by Kevin Blighe 87k • written 8.1 years ago by Amitm ★ 2.2k

0

Entering edit mode

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

ADD REPLY • link 8.1 years ago by star ▴ 350

1

Entering edit mode

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 REPLY • link updated 5.6 years ago by Kevin Blighe 87k • written 8.1 years ago by Amitm ★ 2.2k

Login before adding your answer.