Question: Infer CNVs from SNP variant allele fractions
0
gravatar for ceruleanivy
10 months ago by
ceruleanivy30
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

enter image description here

snp next-gen R • 360 views
ADD COMMENTlink modified 9 months ago by willgilks230 • written 10 months ago by ceruleanivy30
0
gravatar for willgilks
9 months ago by
willgilks230
United Kingdom
willgilks230 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 https://sourceforge.net/projects/excavator2tool/ published a few months ago https://academic.oup.com/nar/article/44/20/e154/2607979/Enhanced-copy-number-variants-detection-from-whole

ADD COMMENTlink written 9 months ago by willgilks230
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1476 users visited in the last hour