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-   -   Allele frequency calculation from cgh data for wes data (http://seqanswers.com/forums/showthread.php?t=27178)

April21 02-05-2013 12:16 PM

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??

DavidShih 07-18-2013 04:27 PM

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


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