Hardware-friendly version of GATK4 HaplotypeCaller.
git clone https://github.com/avis9ditiu/gatk-haplotypecaller-cpp17.git
cd gatk-haplotypecaller-cpp17
mkdir build
cd build
cmake ..
make
./gatk -I ../input/chrM.sam -R ../reference/chrM.fa -O ../output/chrM.vcf