Adding an extra/dummy chromosome to reference genome

Question

[Omurice]

What would be the recommended way to add a dummy/extra chromosome (in this case my vector/plasmid construct sequence) to a human reference genome? I am hoping to pull out reads aligned to this additional chromosome as well (also is there any caveat about me doing something like this?).

Answer 1

[Pierre Lindenbaum]

cat ref.fa plasmid.fa  > newref.fa
samtools faidx newref.fa
samtools dict newref.fa > newref.dict