Question: CNV data from Illumina OncoArray Cheap analysis
0
gravatar for melania 2282
8 weeks ago by
melania 2282100
melania 2282100 wrote:

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

gwas cnv snpchip • 131 views
ADD COMMENTlink written 8 weeks ago by melania 2282100
1

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 REPLYlink written 8 weeks ago by bernatgel2.8k

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 REPLYlink written 8 weeks ago by melania 2282100
1

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.

ADD REPLYlink written 8 weeks ago by bernatgel2.8k
1

Thank you very much bernatgel

ADD REPLYlink written 8 weeks ago by melania 2282100
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