Physical Sciences and Mathematics Commons^™

Blackops: Increasing Confidence In Variant Detection Through Mappability Filtering, Christopher R. Cabanski, Matthew D. Wilkerson, Matthew Soloway, Joel S. Parker, Jinze Liu, Jan F. Prins, J. S. Marron, Charles M. Perou, D. Neil Hayes

Computer Science Faculty Publications

Identifying variants using high-throughput sequencing data is currently a challenge because true biological variants can be indistinguishable from technical artifacts. One source of technical artifact results from incorrectly aligning experimentally observed sequences to their true genomic origin (‘mismapping’) and inferring differences in mismapped sequences to be true variants. We developed BlackOPs, an open-source tool that simulates experimental RNA-seq and DNA whole exome sequences derived from the reference genome, aligns these sequences by custom parameters, detects variants and outputs a blacklist of positions and alleles caused by mismapping. Blacklists contain thousands of artifact variants that are indistinguishable from true variants and, …