Running and Verifying CNVnator

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following commands to create a working directory and go to it:

   mkdir -p /path/to/CASE
   cd /path/to/CASE

3. Download the test case file and use an SFTP tool to upload it to the /path/to/CASE directory.
4. Run the following commands to perform the test:

   { time cnvnator -root B17NC.root -tree B17NC.bam ; } 2>&1 |tee -a Mapping.log
   { time cnvnator -root B17NC.root -his 1000 -fasta chr14.GRCm38.primary_assembly.genome.fa.gz ; } 2>&1 |tee -a Histogram.log
   { time cnvnator -root B17NC.root -stat 1000 ; } 2>&1 |tee -a Statistics.log

   If the command output shown in Figure 1 is displayed, the calculation ends properly.

   Figure 1 Test example