Two sets of SNPs (including positions and nucleostides) are randomly generated, and the simulated maternal and paternal genomes are obtained by modifiying the reference human genome using the simulated SNPs. This is completed by snp_simulate.cpp.
Compilation:
g++ -O3 -std=c++0x snp_simulate.cpp -o snp_simulate
Run:
snp_simulate hg38.fa
hg38.fa is the human reference genome.
Output:
maternal.fa: The simulated maternal genome.
paternal.fa: The simulated paternal genome.
simulated_snp.txt: All the simulated SNPs.
The file simulated_snp.txt in this repository records all the simulated SNPs that were used in our paper.