Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
Fig 2
Example of allele specific CNV calls generated from modified bam files.
A) Genome-wide (left) and chromosome-view (right) of allele specific copy number, BAF and depth ratios for balanced gain of p-arm in chromosome 22 inferred using Sequenza. Blue and red lines show allele specific copy number profiles for each chromosome (lines are offset from discrete copy number values by ± 0.1 for visual separation of the two alleles). The small blue and red spots on the top figure (orange circle) show a balanced gain on p-arm of chromosome 22 (BAF is not affected as a result of balanced gain). Each black dot on the right figures represents a genomic locus and the red lines indicate the inferred value for consecutive segments. B) Allele-specific gain of entire chromosome 21(orange circle). As shown only one copy of the chromosome is gained and hence the allele frequency is reduced from the 0.5 to ~0.33 in the chromosome view. C) Genome-wide (left) and chromosome-view (right) for 36 events (21 gains and 25 losses) sampled from Genome Atlas for Bladder Urothelial Carcinoma (BLCA) for 100% tumor content. As expected depth ratio and BAFs are approximately 0.5 and zero respectively.