LoLoPicker: Detecting Low Allelic-Fraction Variants in Low-Quality Cancer Samples

Summary We developed an efficient tool dedicated to call somatic variants from whole-exome sequencing (WES) data using tumor and its matched normal tissue, plus a user-defined control panel of non-cancer samples. Compared with other methods, we showed superior performance of LoLoPicker with significantly improved specificity. The algorithm of LoLoPicker is particularly useful for calling variants from low-quality cancer samples such as formalin-fixed and paraffinembedded (FFPE) samples. Implementation and Availability The main scripts are implemented in Python 2.7.8 and the package is released at https://github.com/jcarrotzhang/LoLoPicker .