Infer CNVs from SNP variant allele fractions
Entering edit mode
7.1 years ago
ceruleanivy ▴ 50

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

enter image description here

SNP next-gen R • 1.6k views
Entering edit mode
7.1 years ago
willgilks ▴ 360

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


Login before adding your answer.

Traffic: 1565 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6