lhmut is a likelihood-based mutation detector for SNV and small indel.
alglib-3.14.0 (http://www.alglib.net/translator/re/alglib-3.14.0.cpp.gpl.tgz)
git clone https://github.com/RainyEricYe/lhmut.git
cd lhmut
vi Makefile && change lib path
make
Program: lhmut (likelihood-based mutation detector)
Version: v0.2
Authors: Rui YE
Contact: yerui@connect.hku.hk
Options: lhmut -i in.pileup -o outfile
-i [s] input pileup file
-o [s] output mutation file
-q [i] base quality cutoff [20]
-s [i] min support num on each strand [1]
-f [f] min fraction of alterative allele in a read family [1e-5]
-e [f] precision of allele frequency while calculate likelihood ratio [1e-8]
-g [f] gap between likelihood ratios of major and rest genotypes [2.0]
-x [i] Encoding offset for phred quality scores [33]
-d debug mode [false]
-h help
-v version