I know how to download all the vcfs from query the info fields to get allele frequency:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
and I have been doing this. I am wondering if there is a flat file that exits anywhere that has the non-genotype VCF fields or just the allele frequency for each site for different populations. So you can get allele frequency without having to download those big vcfs.
This seem like it would be a handy thing to have so I wonder if I am just missing it.
2 answers
Might look at ALFA
Ref
https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/
Some flatfiles, run bigBedToBed to convert to bed
https://ftp.ncbi.nih.gov/snp/population_frequency/TrackHub/20200227123210/hg38/
Read https://ftp.ncbi.nih.gov/snp/population_frequency/TrackHub/20200227123210/hg38/ALFA.html
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ANNOVAR had compiled something like that, you could install it and pull the datafiles out.