How To Upload A List Of Snp Number And Get Their Minor Allele Frequency As An Txt/Excel File?
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8.8 years ago
Omid ▴ 570

I am analysing exome sequence result. How can I upload a list of snp number(rs...) and get their minor allele frequency as a txt/Excel file?

Thanks

maf • 5.2k views
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the minor allele frequency is always defined relative to a dataset. Do you want to get their MAF in all human populations? Or only in some of them? Or in other species?

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I need MAF in European population.Thanks

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Is that possible to get MAF of SNVs which do not have rsnumber (In European population)? information is (chrN:XXX) Thanks in advance!

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8.8 years ago

You can use the UCSC Table Browser.

  1. Change "group" to "Variation and Repeats"
  2. Change the Track to"Common SNPS (135)"
  3. Change the "Table" to "snp135common"
  4. Click on identifiers: PASTE LIST and past in your rs numbers
  5. Select "get all fields from selected table" as the output format
  6. Click "Get output"

If you need details of what is actually in the table, you can click on the "describe table schema" after step 3 above.

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thanks Sean I found it.

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8.8 years ago

You can also get the MAF from the Biomart portal.

The following instructions are for Biomart version 0.7, because I still haven't learned how to use the newer version.

  • Go to http://www.biomart.org/ and click on Version 0.7->Portal
  • as database, select the latest Ensembl Variation dataset available, and as dataset, select the Human Variation (dbSNP) dataset, or the one for the organism of your interest
  • In Filters, open GENERAL VARIATION FILTERS, select "Filter by Variation ID", and paste your list of SNPs
  • In Attributes, open SEQUENCE VARIATION, and select Minor Allele Frequency and any annotation you may be interested into
  • Click on Results to download the data.
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