LoLoPicker: Detecting Low Allelic-Fraction Variants in Low-Quality Cancer Samples from Whole-exome Sequencing Data

SummaryWe developed an efficient tool dedicated to call somatic variants from next generation sequencing (NGS) data with the help of 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 low allelic-fraction variants from low-quality cancer samples such as formalin-fixed and paraffin-embedded (FFPE) samples.\n\nImplementation and AvailabilityThe main scripts are implemented in Python 2.7.8 and the package is released at https://github.com/jcarrotzhang/LoLoPicker.