Inputs required for CNVnator

Question

[sjlee4019]

As I know, there are three inputs required for running CNVnator.

1. bam files of my samples
2. fasta file of the reference genome
3. fasta file for individual chromosomes

What I'm not sure is if the third file is the individual chromosomes of the reference genome fasta file or fasta files for individual chromosomes of my samples.

I also wonder why the third file is needed when there are first two files.

[Pierre Lindenbaum]

What I'm not sure is if the third file is the individual chromosomes of the reference genome fasta file or fasta files for individual chromosomes of my samples.

it's an individual chromosome from the REF.

cnvnator is a CNV caller, it doesn't care about the SNPs of your samples.