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  • To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X) exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20–100%, 150 BAM files in total). Here we introduce Bamgineer, a tool to modify existing BAM files to precisely model allele-specific and haplotype-phased CNVs (Fig 1). We implemented parallelization of the Bamgineer algorithm for both standalone and high performance computing cluster environments, significantly improving the scalability of the algorithm.
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