A problem in the steps in CNVnator

[yuhao]

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?

[vhtseq]

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:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/

and download fasta files into your working directory.
If you're just working on chromosome 1, only need chr1.fa