SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
how does varscan somatic compute variant allele frequency? genomicist Bioinformatics 0 06-11-2012 03:21 AM
Question on Minor allele Frequency in dbSNP135 ngarg General 0 02-06-2012 09:55 AM
PubMed: Minor variant detection in amplicons using 454 massive parallel pyrosequencin Newsbot! Literature Watch 0 09-13-2011 02:00 AM
how to fetch the snp allele frequency? dzmtnvmt Bioinformatics 3 06-21-2011 03:44 AM
Minor Allele Frequency Cutoff/Threshold BertieWooster Bioinformatics 1 09-28-2009 01:50 PM

Reply
 
Thread Tools
Old 05-07-2013, 10:50 AM   #1
BhariD
Member
 
Location: Georgia

Join Date: Mar 2013
Posts: 15
Default how to compute Minor Allele Frequency for a variant call?

I am interested in computing the minor allele frequency (MAF) for each variant or SNP call in the RNA-seq data obtained from Varscan calling method. Is it as simple as the fraction of number of variant alleles divided by the total number of alleles across all samples for each variant? For example, I have four samples with 4 genotypes for a SNP call

S1 = GG
S2 = GC
S3 = GC
S4 = GG

I computed the variant allele frequency (C) as 2/8 i.e. 0.25. Is this the MAF? I am interested in SNPs < 1% minor allele frequency that are rare, unknown and potentially clinically associated. But I don't think my data set can have MAF of 1% from the way I am computing it. Any suggestions?

bhariD
BhariD is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:39 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO