Is variant masked genome ref required for the alignment ?

[yxian9]

Thanks for providing this awesome tool!

I just want to double-check do I need to use variant masked genome ref when doing the alignment? That's what I read in some allele-specific analysis paper.
Sorry, I do not fully understand how hickit.js resolve the phrase.
Thanks!

[tanlongzhi]

Thank you for your kind words. A variant-masked genome reference is not needed. In fact, the aligner (BWA) cannot accept N-masking information anyway.

[yxian9]

Thank you for the prompt reply!