GRCh37 database, population filter

Question

[gwas_maniac]

Good morning to all! I am here with another question that has been bugging me. I am using the GRCh37 database for SNPs, and those SNPs are taken from 5 big population across the globe. My question is, when I browse the SNPs for example http://grch37.ensembl.org/Homo_sapiens/Transcript/Variation_Transcript/Table?db=core;g=ENSG00000131495;r=5:140018325-140027370;t=ENST00000252102, I can see ALL the SNPs from the 5 populations but I want to know if there is a filter so I can take the SNPs from a particular population and not all of them. Do you happen to know anything?

Answer 1

[trausch]

If you feel comfortable using VCF files then my approach would be to download the 1000 Genomes GRCh37 variants

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/

For every variant, INFO:AF is the global allele frequency and INFO:EAS_AF, EUR_AF, AFR_AF, AMR_AF and SAS_AF are the super-population allele frequencies.

[gwas_maniac]

wow greatly appreciated!

Answer 2

[Emily]

You can use BioMart. There's a help video here. Use the short variation database and filter by gene and variation set to only get specific populations.

[gwas_maniac]

thank you so much!!

[gwas_maniac]

i have also noticed that biomart has two options for every population. eg: EUR and EUR-COMMON. what is the difference between the two?

[Emily]

Common means frequency > 1%.