how to generate PFB file from illumina bovine 777k report for CNV analysis using PennCNV

Question

[anurodh1985]

I have to analyse the CNV from illumina 777k bovine HD SNP array data. I have generates signal intensity files but unable to create the PFB file. How to run compile_pfb.pl program using bovine 777k signal intensity file.

Answer 1

[cge]

Hello, you should run this command (I needed a pfb file for the 170K canine array), for me it worked: ./compile_pfb.pl \ -listfile signal_file_list \ -output OUT170K.pfb

The signal_file_list is just the list of all signal files you have. Make sure that the colums "B Allele Freq" be in this exact format, with: SampleName<space>B<space>Allele<space>Freq

[toglaoshin2121]

@cge Thank you so much! I have tried with the same script but error is coming that invalid header in input file. Can you please specify the types of columns to be included in the input file?