Running and Verifying Beagle

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to go to the /path/to/BEAGLE directory:

   cd /path/to/BEAGLE

3. Run the following commands to create a script file and edit it:
   1. Create a test.sh script file.

      vi test.sh

   2. Press i to enter the insert mode and add the following content to the file:

      #!/bin/sh
      echo
      echo "*** Creating test files: ref.27Apr20.b81.vcf.gz target.27Apr20.b81.vcf.gz ***"
      echo
      zcat test.27Apr20.b81.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.27Apr20.b81.vcf.gz
      zcat test.27Apr20.b81.vcf.gz | cut -f1-9,191-200 | gzip > target.27Apr20.b81.vcf.gz
      
      echo
      echo "*** Running test analysis with \"gt=\" argument ***"
      echo
      java -jar beagle.27Apr20.b81.jar gt=test.27Apr20.b81.vcf.gz out=out.gt
      
      echo
      echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***"
      echo
      java -jar beagle.27Apr20.b81.jar ref=ref.27Apr20.b81.vcf.gz gt=target.27Apr20.b81.vcf.gz out=out.ref
      
      echo
      echo "*** Making \"bref3\" file ***"
      echo
      java -jar bref3.27Apr20.b81.jar ref.27Apr20.b81.vcf.gz > ref.27Apr20.b81.bref3
      
      echo
      echo "*** Running test analysis with \"bref3\" file ***"
      echo
      java -jar beagle.27Apr20.b81.jar ref=ref.27Apr20.b81.bref3 gt=target.27Apr20.b81.vcf.gz out=out.bref3

      

      java -Xmx [ GB ] g -jar beagle.jar [ arguments ]

      • In the preceding command, [GB] indicates the upper limit of the memory pool and [arguments] indicates the arguments separated by spaces.
      • [arguments] must include the two parameters:
        • gt = [file] : specifies a VCF file that contains genotype data for the study sample.
        • out = [character string] : prefix of the output file name.
      • For details about more parameters, see the official document at http://faculty.washington.edu/browning/beagle/beagle_5.1_08Nov19.pdf.
   3. Press Esc, type :wq!, and press Enter to save the file and exit.
4. Run the following command to grant the execute permission on the script:

   chmod a+x test.sh

5. Run the following command to execute the script:

   ./test.sh

   The following is an example of the command output. The command output is also saved to the .log file.

   Cumulative Statistics:
   
   Study markers:           1,356
   
   Haplotype phasing time:        1 second
   Total time:                    1 second
   
   End time: 10:33 AM CST on 09 May 2020
   beagle.27Apr20.b81.jar finished