%0 Journal Article %A Jian Carrot-Zhang %A Jacek Majewski %T LoLoPicker: Detecting Low Allelic-Fraction Variants in Low-Quality Cancer Samples %D 2016 %R 10.1101/043612 %J bioRxiv %P 043612 %X Summary We 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.Implementation and Availability The main scripts are implemented in Python 2.7.8 and the package is released at https://github.com/jcarrotzhang/LoLoPicker. %U https://www.biorxiv.org/content/biorxiv/early/2016/04/24/043612.full.pdf