Hello,

I'm learning how to use PennCNV-Seq (pipeline for variant calling). I've already installed the dependencies (bedtools and pennCNV).

I have to execute the command below but I don't understand it and I can't find a relevant tutorial online. I have the bam file and I know that the fasta file is the reference. However, If I could have a link to download files for simulation it would be great.

This is the command line:

./penncnv-seq_example.sh [penncnv_dir] [penncnv_ref_dir] [genome_version] [population] [reference.fasta] [bam_file]

Thank you