Reverse Complement Human Genome Reference

Question

[L. A. Liggett]

I am using hg19.fa for my alignments and for a particular control I was thinking of running I would like to align to the negative strand of the reference genome. I took the reverse complement of hg19 and then index with bwa index but it will not index. Is there a way to properly do this?

Answer 1

[GenoMax]

Aligners always look at both strands when aligning.

[Cacau]

Yes, perhaps you can do that after mapping by scripts.