SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
Allele frequency calculation in SNP calling Rachelly Bioinformatics 5 05-14-2012 12:07 PM
Variant Frequency Calculation (non-SNP)? dmtruong Bioinformatics 0 12-27-2011 06:53 PM
allele frequency threshold GATK m_elena_bioinfo Introductions 3 12-12-2011 12:29 PM
how to fetch the snp allele frequency? dzmtnvmt Bioinformatics 3 06-21-2011 04:44 AM
Minor Allele Frequency Cutoff/Threshold BertieWooster Bioinformatics 1 09-28-2009 02:50 PM

Reply
 
Thread Tools
Old 02-05-2013, 01:16 PM   #1
April21
Junior Member
 
Location: Phoenix, USA

Join Date: Jan 2013
Posts: 3
Default Allele frequency calculation from cgh data for wes data

Hi
I am trying to analyze exom sequencing data in light of copy number correction.I have corresponding aCGH data for these samples-
Can someone suggest a tool where in I can use CGH data to calculate allele frequency for sequencing mutation results??
April21 is offline   Reply With Quote
Old 07-18-2013, 05:27 PM   #2
DavidShih
Junior Member
 
Location: Toronto

Join Date: Jun 2013
Posts: 1
Default

Instead of "allele frequency", did you mean "clonal frequency" or "cellular multiplicity"?

You can get allele frequency just by dividing the count of the alternate nucleotide by the counts of the alternate and reference nucleotide.

After correcting these allele frequencies for copy-number, ploidy, and purity, you can determine the number of copies of the alleles per tumour cell (clonal frequency or cellular multiplicity).

In most cases, this step requires allele-specific copy-number estimates, which cannot be derived from aCGH data as far as know.

But the ABSOLUTE program does allow the use of total copy-number estimates to calculate both the absolute copy-number and the cellular multiplicity of the SNVs. The results won't be as good as when allele-specific copy-number is available.

See http://www.broadinstitute.org/cancer/cga/absolute
DavidShih 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 12:14 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO