CNV data from Illumina OncoArray Cheap analysis

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3.4 years ago

mel22 ▴ 100

Hello I have two output files from illumina bedcheap contaning results of logR (ratio), B allele frequency, X, Y. Thes files were proceeded with illumina GenomeStudio. Could yo please suggest tools to explore this type of files ?

Thank you very much

SNPchip gwas CNV • 1.0k views

ADD COMMENT • link 3.4 years ago by mel22 ▴ 100

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Hi Melania,

If you want to perform copy-number calling on this data, in addition to logR and BAF you'll need the genomic position of each SNP (or at least its name (rs) so you can then get their position). With that, there are plenty of tools that will call copy-number variants and the most suitable will depend on your sample types (tumors? human?) and your personal preferences.

ADD REPLY • link 3.4 years ago by bernatgel ★ 3.4k

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Thank you barnatgel , Yes I have the position for these SNPs. It's human germline DNA. So could you please suggest me some program for such analysis ?

ADD REPLY • link 3.4 years ago by mel22 ▴ 100

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I don't have much experience with germline CNV analysis with SNP-arrays, but you can try with PennCNV, or if you prefer working on R you can start with genoCN. I'm sure newer tools should be available, though.