Question: What Are The Recommended Tools For De Novo Cnv Analysis?
gravatar for pathaka001
7.8 years ago by
pathaka00110 wrote:

Hi, Does anyone out there have experience with de novo CNV calling in familial trios. I've gotten PennCNV to work for this, but have questions about its quality. I have had some difficulty getting the R bioconductor package for Minimum Distance to work. Thanks for your input.


cnv • 1.8k views
ADD COMMENTlink modified 7.8 years ago by Istvan Albert ♦♦ 85k • written 7.8 years ago by pathaka00110

Hi Anand -- is there a specific question or problem you're having? PennCNV is a good program, I know several labs that use it. What difficulty are you having with bioconductor? What kind of data are you using? Microarray? NGS?

ADD REPLYlink written 7.8 years ago by Alex Paciorkowski3.4k

Hi Alex, I'm just new to the field, and want to make sure I am using the right approach, before investing too much time in this. I'm using microarray data for this right now. I've gotten PennCNV to work, but am not sure if I'm using the correct PFB (population frequency b allele) file. I got a de novo CNV on the first family I ran the analysis on. So, I'm skeptical and will have the biostatistician re-evaluate the locus that I have seen the de novo CNV in. With bioconductor, I'm right at the beginning. Am having a hard time getting the libaries to load up and so on, right now. Thanks and take care,


Also, which groups/individuals/labs do you know that use PennCNV. It might be very productive for me to talk to someone.

ADD REPLYlink written 7.8 years ago by pathaka00110
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1503 users visited in the last hour