Deleted:Ancestral Allele FASTA sequence aligned with Candidate Gene Region

Question

[Warrenkb]

Hello,

I have a .fa file of the entire chromosome 15 of the human ancestor and a candidate gene region located on the same chromosome. I was wondering is if possible to filter the excess gene region so that I can align both .fa files? My region of interest is about 60k base pairs long. I am essentially trying to add the ancestral alleles to the INFO.

If they are any other ways that I can do this, please do share.

Thanks!