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The usage of BAF-LRR plot and concept of canonical positions can also be found in my previous work. This is the penalty for increasing the copy number of the baseline DNA content.
On a BAF-LRR plot with x-axis being |BAF-0.5|, the origin stands for genotype AB.
First, the LRR data obtained from in this fashion usually suffer from technical contraction, for example, the theoretical value for a heterozygous deletion is -1, but due to this artifact, its absolute value is smaller.
If there are K tumor/normal pairs, there should be K VCF files, all saved in the same directory with only these K files in it. It was so tickled that I began to be covered with goose bumps.