How To Call Cnvs From Raw Intensities

Question

[elengss]

Dear all,

Does anyone have any methods for calling CNVs and/or obtaining LRR/BAF from raw intensities?

I have a file that looks like this...with allele specific intensity for each SNP per sample

191291_F03_5104684 191291_F03_5104684 4279 248        653 6601        6286 212        127 7278        172 19881211 1269        658 8445        277 4894        242 3513        274 8954        8391 320        309 6974        6005 935354 4497 14480 178       219 8907        452 7644        342 8866        6461 461        134 4959        789 9631        176 3185 15569 736       256 8832        8123 87 266 8068        10884

And a SNP annotation file with SNPs and positions

I understand that Penn CNV - Affy module can generate LRR/BAF and call CNVs, but it requires quite a lot of other information eg. confidence scores etc. which I don't have

Is there a better way to do this?

Thanks a lot.

ST