LFMD

Low Frequency Mutation Detector

Preparation

• htslib(https://github.com/samtools/htslib)

• SeqLib(https://github.com/walaj/SeqLib)

• alglib(http://www.alglib.net/translator/re/alglib-3.15.0.cpp.gpl.tgz)

• bamRdf(https://github.com/RainyEricYe/bamRdf)

• bamDCS(https://github.com/RainyEricYe/bamDCS)

• lhmut(https://github.com/RainyEricYe/lhmut)

Install

git clone https://github.com/RainyEricYe/lfmd.git
cd lfmd2

cd example; sh test.sh # check if it works

# if not work, please export PATH to needed libs, retest
# or compile it as follows.
cd ..
vi install.sh
# modify paths to SeqLib alglib and librarys    
sh install.sh
cd example; sh test.sh

Contact

yerui@connect.hku.hk

Citation

Rui Ye et al. LFMD: detecting low-frequency mutations in genome sequencing data without molecular tags. https://www.biorxiv.org/content/10.1101/617381v11

Usage

vi lfmd.sh && ajust parameters and file paths
./lfmd.sh in.sortByReadID.bam outprefix