Body: <p>I want to assess ploidy estimation (i.e., diploid vs tetraploid) in a set of samples for which I have both results from the variant caller (i.e., SNVs) and from the copy number caller.</p>
  <p>What are the possible approaches that can be used in this case? I know that in some in cases it might be possible to use VAF to assess ploidy estimation, but I haven't found exactly how this (possibly simple) approach is defined.</p>
  <p>Note: I already have a caller that I am testing. My question is more related to exploratory data analysis or manual inspection of the caller's results.</p>
  <p>VAF distribution examples might be similar to what is done in <a href="https://caravagnalab.github.io/CNAqc/articles/a7_example_MSeq.html#peak-detection" rel="nofollow noreferrer">CNAqc</a> (image below extracted from their online tutorial):
  <a href="https://i.sstatic.net/nEjvZ.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/nEjvZ.png" alt="VAF distribution" /></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-03-03T03:42:07.750Z
Comments.Text: What is the underlying data quality? Would you be able to go in and visually confirm alleles in a single sample in IGV or whatever? Approaches such as [here](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2128-z) use allele frequency at heterozygous SNPs in single samples to try to address this question, so I think that's the relevant question. I have to say that I don't understand the figure or the tutorial at first glance, it appears to be looking for de novo mutations (?) and seeing their frequency.
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-03-03T18:41:36.900Z
Comments.Text: Thank you. I have updated the question regarding the tutorial - I'm only interested in plotting the VAF distribution for the different genotypes, that is the first example I could find online to explain one of the tools for the analysis (sorry it that confused you). I will read the paper you linked, thank you.
Comments.UserDisplayName: gc5
Tags: <vcf><snp><variant-calling><cnv><allele-frequency>
Title: Assess ploidy estimation through SNV and CNV results
ThreadText: # Assess ploidy estimation through SNV and CNV results
  
  (Asked by: username_0 on 2022-03-01)
  
  I want to assess ploidy estimation (i.e., diploid vs tetraploid) in a set of samples for which I have both results from the variant caller (i.e., SNVs) and from the copy number caller.
  
  What are the possible approaches that can be used in this case? I know that in some in cases it might be possible to use VAF to assess ploidy estimation, but I haven't found exactly how this (possibly simple) approach is defined.
  
  Note: I already have a caller that I am testing. My question is more related to exploratory data analysis or manual inspection of the caller's results.
  
  VAF distribution examples might be similar to what is done in [CNAqc](https://caravagnalab.github.io/CNAqc/articles/a7_example_MSeq.html#peak-detection) (image below extracted from their online tutorial):
  [![VAF distribution](https://i.sstatic.net/nEjvZ.png)](https://i.sstatic.net/nEjvZ.png)
  
  **Tags:** vcf, snp, variant-calling, cnv, allele-frequency
  
  > **Comments:**
  > **username_1**: What is the underlying data quality? Would you be able to go in and visually confirm alleles in a single sample in IGV or whatever? Approaches such as [here](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2128-z) use allele frequency at heterozygous SNPs in single samples to try to address this question, so I think that's the relevant question. I have to say that I don't understand the figure or the tutorial at first glance, it appears to be looking for de novo mutations (?) and seeing their frequency.  
  > **username_0**: Thank you. I have updated the question regarding the tutorial - I'm only interested in plotting the VAF distribution for the different genotypes, that is the first example I could find online to explain one of the tools for the analysis (sorry it that confused you). I will read the paper you linked, thank you.  
  
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  ## 0 answers
  
  