LoLoPicker: detecting low allelic-fraction variants from low-quality cancer samples.

ABSTRACT:

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 particul

SUBMITTER: Carrot-Zhang J 

PROVIDER: S-EPMC5514890 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature