Cancer genomics analysis Tools

Bamgineer is a tool that can be used to introduce user-defined haplotype-phased allele-specific copy number variations (CNV) into an existing Binary Alignment Mapping (BAM) file with demonstrated applicability to simulate somatic cancer CNVs in phased whole-genome sequencing datsets. This is done by introducing new read pairs sampled from existing reads, thereby retaining biases of the original data such as local coverage, strand bias, and insert size. As input, Bamgineer requires a BAM file and a list of non-overlapping genomic coordinates to introduce allele-specific gains and losses. We implemented parallelization of the Bamgineer algorithm for both standalone and high performance computing cluster environments, significantly improving the scalability of the algorithm. Bamgineer has been extensively tested on phased, whole-genome sequencing samples.