Running and Verifying XHMM

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Download the test case package POST_GATK_DATA.zip.
3. Use an SFTP tool to upload the test case package to the /path/to/TEST directory on the server.
4. Run the following commands to decompress the test case package:

   cd /path/to/TEST
   unzip POST_GATK_DATA.zip

5. Run the following commands to merge multiple samples (at the same point) output by GATK depths using XHMM:

   xhmm --mergeGATKdepths -o ./DATA.RD.txt \
   --GATKdepths group1.DATA.sample_interval_summary \
   --GATKdepths group2.DATA.sample_interval_summary \
   --GATKdepths group3.DATA.sample_interval_summary

   The execution result is as follows:

   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   Command-line parameter values:
   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   mergeGATKdepths
   GATKdepths="group1.DATA.sample_interval_summary"
   GATKdepths="group2.DATA.sample_interval_summary"
   GATKdepths="group3.DATA.sample_interval_summary"
   outputMatrix="./DATA.RD.txt"
   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   
   Reading GATK depth file group1.DATA.sample_interval_summary
   Reading GATK depth file group2.DATA.sample_interval_summary
   Reading GATK depth file group3.DATA.sample_interval_summary
   Writing GATK read-depth matrix of 30 samples by 300 targets to ./DATA.RD.txt
   
   Total CPU time for processing this job: 6 seconds
   [user time: 6
   system time: 0
   children user time: 0
   children system time: 0]
   Total time for processing this job: 0 seconds

   Generated file:

   DATA.RD.txt