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Minor allele frequency
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2.3 years ago
@alessandrotestori724364

Hi. I have plenty of SNPs and I want to get their mafs. Is there a file somewhere I can download with this information? I have already tried SNIPA, Haploreg and dbSNP, but the problem is that I cannot find all of my SNPs because some of them have aliases. Please let me know. Thanks, Alessandro.

GWAS SNPs Alleles • 803 views
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Does this previous post help? You may need to update the builds as this post is a few years old, but the process is the same.

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Unfortunately some SNPs are missing in UCSC or dbSNP; probably the SNPs in my list have been merged to other SNPs with another name (have been "renamed").

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Are you just looking for something that will output SNPs and their AFs that have an allele frequency above a specific value? I wrote a parser that will iterate through a vcf file and can output AFs which can be ordered.

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My problem is that I cannot find a database which I can download as a text file with all the SNPs I need and information about allele frequency: unfortunately some of my SNPs are probably aliases.

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Then what is the format of your SNPs? How is the notation? Which identifiers?

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Just a column with rs identifiers:

rs10503665\nrs8130815\nrs4822193

....

Around 25.000 rs identifiers

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the snp IDs you have ('rs\d+') are dbSNP accession IDs - do you know what release of dbSNP (132, 135, ...) your collection of SNPs are derived from? What percentage of your SNPs are you failing to find a MAF for?

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Unfortunately I don't know the dsSNP release. I fail to find around 2% of my SNPs. I need a database to access where I can find all SNPs and aliases. Best if I can download it locally.

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This makes sense to me (others may disagree). A small number of SNPs will fail to match for reasons you have already mentioned; dbSNP IDs get retracted or moved. If you knew the base-pair coordinates or the dbSNP release this would be easier. Because you do not know, you could; i) try to get this info, ii) try to match the 2% that fail to previous releases of dbSNP, iii) accept that 2% 'got away' and move on.

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98% successful? That's pretty good :-) If you would download or query different versions of dbSNPyou could try to hunt down in which release those 2% were present.

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