I want to use PennCNV to call CNV from Brassica napus 60K Illumina Infinium SNP array, and this array belongs to Plant data.
My problem is that in the CNV calling step, I do not have PFB file. I used the command { compile_pfb.pl -listfile sampleID.txt -output try.pfb}, but always gave me the error message:
Use of uninitialized value $snp in pattern match (m//) at /home/PennCNV-1.0.5/compile_pfb.pl line 128.
Use of uninitialized value $snp in hash element at /home/PennCNV-1.0.5/compile_pfb.pl line 140.
I put all my sample list in sampleID.txt file, and I used kcolumn.pl to get sample.split files with format like this:
Name Chr Start GType B Allele Freq Log R Ratio
Bn-A01-p10000230 A01 9939082 NC 0.1834546 1
Bn-A01-p1000115 A01 1035075 AB 0.7641979 0.5432846
Bn-A01-p1001022 A01 1035881 BB 0.1459281 1
Bn-A01-p10026020 A01 9977378 NC 0.1002549 0.00
I tried several times, but still, could you help me check it?
Hi Dr. Wang,
I want to use PennCNV to call CNV from Brassica napus 60K Illumina Infinium SNP array, and this array belongs to Plant data. My problem is that in the CNV calling step, I do not have PFB file. I used the command { compile_pfb.pl -listfile sampleID.txt -output try.pfb}, but always gave me the error message:
Use of uninitialized value $snp in pattern match (m//) at /home/PennCNV-1.0.5/compile_pfb.pl line 128. Use of uninitialized value $snp in hash element at /home/PennCNV-1.0.5/compile_pfb.pl line 140.
I put all my sample list in sampleID.txt file, and I used kcolumn.pl to get sample.split files with format like this: Name Chr Start GType B Allele Freq Log R Ratio Bn-A01-p10000230 A01 9939082 NC 0.1834546 1 Bn-A01-p1000115 A01 1035075 AB 0.7641979 0.5432846 Bn-A01-p1001022 A01 1035881 BB 0.1459281 1 Bn-A01-p10026020 A01 9977378 NC 0.1002549 0.00
I tried several times, but still, could you help me check it?
Best Wishes! ling