PGDSpider

Owned by Simon Alexander, created
Last updated: Dec 23, 2022
1 min read
1 Overview | 2 Using | 2.1 Multicore

Overview

  • PGDSpider: PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs.

Using

Use the module name pgdspider to discover versions available and to load the application.

The application provides two components:

  1. A command line: Using pgdspider from the command line.

  2. A GUI:

    • Start an interactive desktop from the OnDemand/SouthPass service.

    • Open a terminal and load the pgdspider module.

    • Call pgdspider-gui from the command line.

The general form of the command line is:

pgdspider -inputfile example_SAM.sam -inputformat SAM -outputfile output.vcf -outputformat VCF -spid sam_to_vcf.spid

What we have noticed is that:

  • The output file must be post fixed with the file format e.g. as above .vcf

  • A spid file must be defined. As suggested within the manual, you can use the GUI to create and test this, and then save out to a file. So for example, the spid file is where you will define the required SAM reference file for the example above.

Multicore

We are not aware the pgdspider applications can run across multiple cores.