I'm trying to generate CNVs using Varscan2. But it does not seem to compile for me. I'm doing the exact command given from the website.
samtools mpileup -q 1 -f human_hg19.fa ~/Normal/BAM/normalfile.bam ~Tumor/BAM/tumorfile.bam | java -jar VarScan.v2.3.1.jar copynumber varscan_cnv_output --mpileup 1
It gives the following output and stops.
Min coverage: 10 Min avg qual: 15 P-value thresh: 0.01 File not found: varscan_cnv_output [mpileup] 2 samples in 2 input files <mpileup> Set max per-file depth to 4000
I'm not sure, what the problem is. Can anyone help? Thanks!
I got this command from the recommended workflow of the website. Here is the link.