These are the files of a reference genome you used to align.
Example: if you're using the human hg19 then you can take a look this link:
and download fasta files into your working directory.
If you're just working on chromosome 1, only need chr1.fa
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A problem in the steps in CNVnator
For the second step in running CNVnator, I see from the README that:
Files with chromosome sequences are required and should reside in running directory or directory specified by -d option. Files should be named as: chr1.fa, chr2.fa, etc.
I am wondering what the file mean? Is it the file for reference sequence?
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