sorry if this is naive but my cnv analysis which I did using ECOLE only has ECOLE prediction whether its a duplication or a deletion and I had read counts of alleles in all positions from my BAM files. how do I obtain major CN and minor CN from this. my samples are cancer whole exome seq. (I also have deepvariant vcf files for snps which contains AD, DP, GT and VAF etc in the info fields)
sorry if this is naive but my cnv analysis which I did using ECOLE only has ECOLE prediction whether its a duplication or a deletion and I had read counts of alleles in all positions from my BAM files. how do I obtain major CN and minor CN from this. my samples are cancer whole exome seq. (I also have deepvariant vcf files for snps which contains AD, DP, GT and VAF etc in the info fields)