Best way to combine sequence data from two genomes?

[adaptivegenome]

Guys,

Sorry for the possibly naive question, but I have two genomes sequenced by Illumina. Each is supposedly homozygous due to inbreeding. I want to combine the two genomes together to simulate heterozygosity.

I made BAM files of each genome using BWA.

I suppose I could use "samtools merge" to combine the two BAM files but is this really fair? Is there a better way to do this, perhaps at the level of BWA?

Thanks!