SNP Allele frequency data

[lre1234]

Hi All,
I have a list of a few thousands SNP that I am trying to get the population allele frequency data for. Ideally, I would like the frequencies for all 26 of the populations within the 1000 genomes for these. I can't seem to find the information anywhere. Does anyone know where I may be able to get this?
Thanks for your help

[Emily_Ensembl]

You could try the Ensembl REST API variation POST endpoint. You'd need to chunk your list of variants into 200s but it would be relatively easy.

[lre1234]

Thanks Emily_Ensembl.
This API does work, but I am still looking to get the allele frequencies for all 26 subpopulations of the 1000 Genomes. This API seems to only give the main continental ancestries. I know that I can probably download all of the genotype information and calculate these myself, but I would have thought there would be a simple way too download the information from somewhere.

[Emily_Ensembl]

pops=1 should get you all 26 populations

[lre1234]

Then I must be doing something wrong (quite likely ) . I'm trying it with the wget example:

wget -q --header='Content-type:application/json' --header='Accept:application/json' \
--post-data='{ "ids" : ["rs56116432" ] }' \
'http://rest.ensembl.org/variation/homo_sapiens' -O temp.out pops=1

And only get this as the output:

{"rs56116432":{"ambiguity":"Y","ancestral_allele":null,"minor_allele":"T","mappings":[{"allele_string":"C/T","start":133256042,"coord_system":"chromosome","assembly_name":"GRCh38","end":133256042,"strand":1,"seq_region_name":"9","location":"9:133256042-133256042"},{"strand":1,"seq_region_name":"CHR_HG2030_PATCH","end":133256189,"assembly_name":"GRCh38","location":"CHR_HG2030_PATCH:133256189-133256189","allele_string":"C/T","coord_system":"chromosome","start":133256189}],"MAF":0.00259585,"most_severe_consequence":"missense_variant","synonyms":["NM_020469.2:c.689G>A","NP_065202.2.Gly230Asp"],"evidence":["Frequency","1000Genomes","ESP","ExAC","TOPMed","gnomAD"],"source":"Variants (including SNPs and indels) imported from dbSNP","var_class":"SNP","name":"rs56116432"}}

I've also tried it with other SNPs just to see if it was a SNP specific thing, but get similar outputs.

[lre1234]

Then I must be doing something wrong (highly probable ). I'm trying it with the wget example:

wget -q --header='Content-type:application/json' --header='Accept:application/json' \
--post-data='{ "ids" : ["rs56116432" ] }' \
'http://rest.ensembl.org/variation/homo_sapiens' -O temp.out pops=1

And I get:

{"rs56116432":{"ambiguity":"Y","ancestral_allele":null,"minor_allele":"T","mappings":[{"allele_string":"C/T","start":133256042,"coord_system":"chromosome","assembly_name":"GRCh38","end":133256042,"strand":1,"seq_region_name":"9","location":"9:133256042-133256042"},{"strand":1,"seq_region_name":"CHR_HG2030_PATCH","end":133256189,"assembly_name":"GRCh38","location":"CHR_HG2030_PATCH:133256189-133256189","allele_string":"C/T","coord_system":"chromosome","start":133256189}],"MAF":0.00259585,"most_severe_consequence":"missense_variant","synonyms":["NM_020469.2:c.689G>A","NP_065202.2.Gly230Asp"],"evidence":["Frequency","1000Genomes","ESP","ExAC","TOPMed","gnomAD"],"source":"Variants (including SNPs and indels) imported from dbSNP","var_class":"SNP","name":"rs56116432"}}

Unless I'm missing something in the output, all I see is the total MAF and not broken down by populations. I've also tried this with other SNPs and get similar results.

[Emily_Ensembl]

Try adding pops=1 to the URL, like:

wget -q --header='Content-type:application/json' --header='Accept:application/json' --post-data='{ "ids" : ["rs56116432" ] }' 'http://rest.ensembl.org/variation/homo_sapiens?pops=1' -O temp.out

[lre1234]

That works. Thanks. I have a couple thousand to get the frequency for, so I can write some sort of wrap to let it go on and do them all.

One last question, is there a way to limit the output to just the 1000 genomes populations only?

[Emily_Ensembl]

No, you would need to parse your query response to limit the data in that way.