Running and Verifying VarScan

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Copy the test case files and go to the test directory.

   cp hg19.fa /path/to/VARSCAN/varscan-2.4.2
   cp bwa.sam /path/to/VARSCAN/varscan-2.4.2
   cd /path/to/VARSCAN/varscan-2.4.2

3. Use Samtools to convert the format and sort the data.

   samtools view -bS bwa.sam > bwa.bam
   samtools sort -@96 -o bwa.sort.bam bwa.bam

4. Use Samtools to process the test case files.

   samtools mpileup -f hg19.fa bwa.sort.bam > myData.pileup

5. Execute the test case.

   { time java -jar VarScan.v2.4.2.jar pileup2snp myData.pileup > VarScan.vcf ; } 2>&1 |tee varscan.log

   After the execution is complete, the VarScan.vcf and varscan.log files are generated in the current directory. VarScan.vcf is the case comparison result file and varscan.log is the run log file.

   Check the value of real (in seconds) in the varscan.log file. A smaller value indicates higher performance.

   Figure 1 is an example of the output result.

   Figure 1 An example result