Running HPVDetector in command line mode:

HPVDetector can be executed from command line of Linux/Unix systems. Edit the config.txt file in root directory of HPVDetector to make changes of the variables/path required for the tool. There should be no changes made other than following:
1.mode should be specified as “Integration” or “QuickDetect”
     Ex.: mode=QuickDetect
2.bwa should be specified as path to the BWA 0.6.2 executable
     Ex.: bwa=/home/bwa-0.6.2/bwa
3.picard should be specified as path to the Picard tool 1.100 directory
     Ex.: picard=/home/HPVDetector_v1.0/picard-tools-1.100/
4.hpv_bwa_index should be specified as path to HPV_index_files supplied with the tool
     Ex.: hpv_bwa_index=/home/ HPVDetector_v1.0/HPV_index_files/HPV_143types_EBVref
5.hpv_human_bwa_index should be specified as path to Human_HPV_index_files supplied with the tool
     Ex.: hpv_human_bwa_index=/home/HPVDetector_v1.0/Human_HPV_index_files/human_HPV
6.annotation_dir should be specified as path to annotation_files supplied with the tool
     Ex.: annotation_dir=/home/HPVDetector_v1.0/annotation_files/
7.threads should be specified as whole number (should not exceed the actual number of threads available in the system)
     Ex.: threads=4
8.After making above changes, execute HPVDetector as:
     ./HPVDetector config.txt
9. could be WGS, Transcriptome or Exome
     Ex.: ./HPVDetector config.txt /siha/read_1.fastq /siha/read_2.fastq WGS /siha_output