Does any one have a recommendation of a method or a program to convert X and Y intensities from a genotyping final report text file to their Log R ratio and B allele frequency estimates.
The LRR and BAF were not provided in the final report and I dont have access to Illumina Beadstudio. I was hoping to complete cnv analysis if possible
Any help appreciated.
Final report file format
[Header] GSGT Version 1.9.4 Processing Date 6/19/2015 11:59 AM Content IDBv2_15051423_C.bpm Num SNPs 16223 Total SNPs 18004 Num Samples 41 Total Samples 576 [Data] SNP Name Sample ID Allele1 - Forward Allele2 - Forward Allele1 - AB Allele2 - AB Allele1 - Top Allele2 - Top GC Score X Y ARS-BFGL-BAC-10972 1234 G C A B C G 0.8651 0.726 0.905 ARS-BFGL-BAC-10975 1235 A A A A A A 0.9303 0.983 0.060 ARS-BFGL-BAC-11025 1236 T G A B A C 0.9092 0.434 0.684