I am new to CNV analysis and Vcf file conversion.
I have an Illumina text report and I am looking for a solution how can I convert them into a vcf file(with BAF and LRR) for copy number variation analysis by using bcftools/cnv
my input file looks like:
[Header] GSGT Version 1.9.4 Processing Date 3/6/2014 10:39 AM Content humancore-12v1-0_a.bpm Num SNPs 298930 Total SNPs 298930 Num Samples 24 Total Samples 24 File 7 of 24 [Data] Sample Index Sample ID Sample Name SNP Index SNP Name Chr Position GT Score GC Score Allele1 - AB Allele2 - AB Allele1 - Top Allele2 - Top Allele1 - Forward Allele2 - Forward Allele1 - Design Allele2 - Design Theta R X Raw Y Raw X Y B Allele Freq Log R Ratio SNP Aux SNP ILMN Strand Top Genomic Sequence Customer Strand
Thanks in Advance