LoLoPicker: detecting low allelic-fraction variants from low-quality cancer samples
نویسندگان
چکیده
INTRODUCTION Although several programs are designed to identify variants with low allelic-fraction, further improvement is needed, especially to push the detection limit of low allelic-faction variants in low-quality, "noisy" tumor samples. RESULTS We developed LoLoPicker, an efficient tool dedicated to calling somatic variants from next-generation sequencing (NGS) data of tumor sample against the matched normal sample plus a user-defined control panel of additional normal samples. The control panel allows accurately estimating background error rate and therefore ensures high-accuracy mutation detection. CONCLUSIONS Compared to other methods, we showed a 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 and the package is released at https://github.com/jcarrotzhang/LoLoPicker.
منابع مشابه
LoLoPicker: Detecting Low Allelic-Fraction Variants in Low-Quality Cancer Samples from Whole-exome Sequencing Data
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 varia...
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عنوان ژورنال:
دوره 8 شماره
صفحات -
تاریخ انتشار 2017