RT Journal Article
SR Electronic
T1 LoLoPicker: Detecting Low-Fraction Variants in Low-Quality Cancer Samples from Whole-exome Sequencing Data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 043612
DO 10.1101/043612
A1 Jian Carrot-Zhang
A1 Jacek Majewski
YR 2016
UL http://biorxiv.org/content/early/2016/03/16/043612.abstract
AB 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. We showed superior performance of LoLoPicker with significantly improved specificity, especially for low-quality cancer samples such as formalin-fixed and paraffinembedded (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.