Ignoring copy number when calculating VAF

I was trying to use Variant Allele Frequency (VAF) to analyse tumour heterogeneity but I saw basically I have no copy number neutral variants

In this situation what is the solution? Can I trust VAF ignoring my CN data?

Thank you for any information

r copy number variant allele frequency

• 1,388 views • link

written 6.5 years ago by zizigolu

0 answers

No answers yet.

More posts like this

Strelka calculate vaf usign ICAMS
written 6.1 years ago by parvathi.sudha •

Hi, Has anyone tried the R package "ICAMS" for calculating vaf (variant allele frequency) of strelka variants? I am having issues in reading the vcf …
How we know if mutations in a cluster are clonal or sub-clonal
written 6.3 years ago by zizigolu

Hi I have found a sciclone output via internet like attached [sciclone_out.txt](https://github.com/genome/sciclone/files/4584319/sciclone_out.txt) > head(sciclone_out[1:2,]) chr st Time_1.ref Time_1.var Time_1.vaf Time_1.cn Time_1.cleancn 1 1 160771583 8788 …
I need help with some explanation
written 6.3 years ago by zizigolu

Hi For each variant, the `variant allele frequency (VAF)` depends on the local copy number of the tumor `(CPNmut)`, the `purity (p)`, the local copy …
PennCNV-Affy BAF and LogR position notation for SNP6 data: SNP_A vs CN
written 6.3 years ago by lm687

I would be grateful if someone could point me to an explanation of the meaning of the two different types of rows in BAF and …
Is this range of VAF is ordinary?
written 6.6 years ago by zizigolu

Hi I have calculated `Variant Allele Frequency (VAF)` for called SNVs and INDELs called by Strelka separately. For getting VAF, I done VAF = Tumour …
Some interpretation of Strelka output
written 6.6 years ago by zizigolu

Hi I have called INDELs for tumor/matched normal by Strelka caller In .vcf header I have ##FORMAT=<ID=TAR,Number=2,Type=Integer,Description="Reads strongly supporting alternate allele for tiers 1,2"> ##FORMAT=<ID=TIR,Number=2,Type=Integer,Description="Reads …
It is normal to get nothing for VAF field for INDEL
written 6.6 years ago by zizigolu

HI I calculated variant allele frequency for my INDELs (.vcf file) but returned empty field like below Chrom Position Ref Alt TumorReadCount TumorVariantAlleleCount TumorReferenceAlleleCount NormalReadCount …
How to understand the mutant allele frequency
written 6.8 years ago by 18982289189 •

I am fairly new to this field，and right now I am working with variant allele frequency for cancer genome,data is from cbioportal. I have read …
Single Sample Tumour/Neoantigen Heterogeneity/Clonal Analysis & Phylogenetic Trees
written 6.8 years ago by TLOA3 •

Hi there! There are many programs out there to analyze tumour heterogeneity from multiregion sequencing (i.e. where multiple regions of a tumour are sequenced). Does …
Running sciClone on cell prevalence (CP) data
written 10.5 years ago by marki

Hi, As I understand, sciClone uses estimates of variant allele frequency (VAF) in copy-neutral regions to estimate subclonality (thus, in a manner, not using CNV …