Running Docker with Swiss Army Knife

Here is the overview of Swiss Army Knife

To use an gatk image (made in previous sections) with the Swiss Army Knife tool, you will do the following:

Command Line

dx run app-swiss-army-knife -iimage_file="gatk.tar.gz" -iin="data/mock.vcf" -icmd="gatk SelectVariants -V mock.vcf -O selected.snp.vcf –select-type-to-include "SNP""

From there, this will be what the command line prompts will be:

From there, you will see the job log of the Swiss Army Knife App.

Resources

Full Documentation

To create a support ticket if there are technical issues:

1. Go to the Help header (same section where Projects and Tools are) inside the platform

2. Select "Contact Support"

3. Fill in the Subject and Message to submit a support ticket.