GitHub - shenjia1/gatk-cpp: Hardware-friendly version of GATK4 HaplotypeCaller.

Introduction

Hardware-friendly version of GATK4 HaplotypeCaller.

mkdir build
cd build
cmake ..
make
./gatk -I ../input/chrM.sam -R ../reference/chrM.fa -O ../output/chrM.vcf

Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
native		native
parser		parser
CMakeLists.txt		CMakeLists.txt
README.md		README.md
assembler.hpp		assembler.hpp
cigar.hpp		cigar.hpp
genetyper.hpp		genetyper.hpp
graph_wrapper.hpp		graph_wrapper.hpp
haplotype.hpp		haplotype.hpp
intel_pairhmm.hpp		intel_pairhmm.hpp
interval.hpp		interval.hpp
main.cpp		main.cpp
math_utils.hpp		math_utils.hpp
pairhmm.hpp		pairhmm.hpp
quality_utils.hpp		quality_utils.hpp
read_clipper.hpp		read_clipper.hpp
read_filter.hpp		read_filter.hpp
sam.hpp		sam.hpp
smithwaterman.hpp		smithwaterman.hpp
variant.hpp		variant.hpp