Question: How To Upload A List Of Snp Number And Get Their Minor Allele Frequency As An Txt/Excel File?
1
gravatar for Omid
7.9 years ago by
Omid560
Netherlands
Omid560 wrote:

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 • 4.8k views
ADD COMMENTlink modified 7.9 years ago by Giovanni M Dall'Olio27k • written 7.9 years ago by Omid560

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?

ADD REPLYlink written 7.9 years ago by Giovanni M Dall'Olio27k

I need MAF in European population.Thanks

ADD REPLYlink modified 7.9 years ago • written 7.9 years ago by Omid560

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

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by b.lin0
6
gravatar for Sean Davis
7.9 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

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.

ADD COMMENTlink written 7.9 years ago by Sean Davis26k

thanks Sean I found it.

ADD REPLYlink modified 7.9 years ago • written 7.9 years ago by Omid560
1
gravatar for Giovanni M Dall'Olio
7.9 years ago by
London, UK
Giovanni M Dall'Olio27k wrote:

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.
ADD COMMENTlink written 7.9 years ago by Giovanni M Dall'Olio27k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 875 users visited in the last hour