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

By Jian Carrot-Zhang, Loydie A Jerome-Majewska

Posted 15 Mar 2016
bioRxiv DOI: 10.1101/043612 (published DOI: 10.18632/oncotarget.16144)

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.

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