The scripts to generated simulated data are in this folder.
To simulate paired-end data, run simu.hla.sh like:
Simulation HLA capture reads for HLA Typing
USAGE: <PATH-TO>/simu.hla.sh -n <sample_size> -r <read_length> -1 <depth of haplotype1> -2 <depth of haplotype2>
-n : sample size of simulation [required]
-r : read length [required]
-1 : depth of haplotype1 [required]
-2 : depth of haplotype2 [required]
To simulate different sequencing protocols, use sim_diff_platforms.py.