Preprint on filtering genetic variants in cancer

By | September 13, 2017

Our recent work with Erik Knudsen on variant calling in tumors is now on bioRxiv. The paper introduces a new approach for analyzing genetic variants called from next-gen sequencing of tumors. A key challenge in such sequencing is spurious variants calls, particularly when sequencing tumors that have been xenografted into mice. We introduce and characterize a simple BLAST-based algorithm for removing spurious calls caused by mouse contamination or paralogs in the genome. This algorithm is as effective as much more computationally or bioinformatically intense approaches. Our testing also revealed biases that may be introduced by commonly used variant callers, an important caution for the community. Congratulations Brian!