Explore CNV data from illumina Array

Question

[mel22]

Hello, I have received out put from OncoArray illumina array of CNV data.
The file is a .txt like this :

Sample_ID     Sample_1           Sample_2              Sample_3
variant_1   logR AlleleB X Y    logR AlleleB X Y    logR AlleleB X Y
variant_2   logR AlleleB X Y    logR AlleleB X Y    logR AlleleB X Y
variant_2   logR AlleleB X Y    logR AlleleB X Y    logR AlleleB X Y

Each sample has one column, inside this colum 4 values are space separeted.
I would like to know if there is any CNV exploring program (Like PennCNV) that could accept this file as input ? I already extracted the B allele and log R separatly for all sample but I would like to explore the results more with specialised programs especially visually ... Do you have any suggestion ?

Thank you very much

Answer 1

[bernatgel]

If you have a file for each sample, you can use the R/Bioconductor package CopyNumberPlots to create plots of your raw data and if you call copy number variants (with PennCNV or any other) you can also plot the calls along your data.

[mel22]

Thank you, but PennCNV have a very special input, do you know any other program that i can test it ? thanks

[bernatgel]

If it's cancer samples, you can try with ASCAT, if it's germline data, then maybe DNAcopy or GenoCN?