How is the WGSIM read simulator used to sequence a simulated genome at 5X haploid coverage?

Question

[zhangz.cs]

What is haploid coverage? What argument is used to control producing haploid coverage instead of diploid coverage?

I know the -h option can enable the haploid mode, but I can't understand what the haploid mode really means. I hope someone can help me to answer these questions. Thanks!

Best Regards,
Zhen

Answer 1

[Pierre Lindenbaum]

haploid coverage: there is only one copy of a chromosome: you should only get homozygotes ALT variants.