I have a list of snps (rs-id) in a .txt file. Say it contains many snps. I want to get their minor allele frequency (MAF) for a specific population (e.g. 1000Genomes - Europe, not Global).
The NCBI batch query service is down since a long time ago. Now, it has changed to an API: Variation Services. But the "frequency" service is still under construction. Then I downloaded all data from dbSNP directly and hoped to query it locally. The best I can get is still just the Global MAF, not for some specific population like Europe.
I also tried some R packages like "Rsnps" but similarly they work fine for getting global MAF, not European MAF. If there are such packages available, please tell me to have try and I appreciate a lot.
Finally, I moved to web scrapping and directly query the NCBI website (append rs-id to "https://www.ncbi.nlm.nih.gov/snp/" and get the 1000Genomes-Europe-MAF). Obviously, there is a limit on your query speed and the best is 3 times / sec. Otherwise it will cause an error from NCBI server. If the amount of snps becomes very large, then this method is unrealistic (For 1 million snps, it needs 20 days).
Do you have any suggestions on how to get the MAF for a specific population? Thank you very much for your help.