Question: Infer CNVs from SNP variant allele fractions
gravatar for ceruleanivy
4.1 years ago by
ceruleanivy30 wrote:

I am currently working on data obtained from proton sequencing (IonTorrent) on bulk tumor micro FFPE samples, using panels for exome targeting. Although I've came across some literature on that issue I am not quite experienced so I would like to ask what are the most popular algorithms/software on inferring copy number variations (CNVs) from single nucleotide polymorphism (SNP) variant allele frequencies (VAFs). Here's an example of my data

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snp next-gen R • 1.1k views
ADD COMMENTlink modified 4.1 years ago by willgilks310 • written 4.1 years ago by ceruleanivy30
gravatar for willgilks
4.1 years ago by
United Kingdom
willgilks310 wrote:

Hi ceruleanivy,

In R you might be able to do this using dplyr/tidyr functions.

  1. Convert the data to long format (sample-snpid-depth1-depth2-genotype).
  2. Calculate the allelic depth ratios in a new column.
  3. Standardise the distributions of the two alleles.
  4. Split data fram by genotype
  5. group_by(snpid)
  6. Test for standardised depth ratios for normal distribution.
  7. Bin the results into windows of 100Kb first, to see if any big deletions/duplications show-up.

..or try this program published a few months ago

ADD COMMENTlink written 4.1 years ago by willgilks310
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