Quick StartΒΆ

This is a simple tutorial on how to use the four Jacquard commands.

  1. Install Jacquard (see Installing Jaquard ).

  1. Unzip the examples.zip file to your home directory (or other directory of your choice).

    The examples directory contains sample input VCFs from five patients run with three variant callers. The input VCFs are based on a subset of actual variant calls from clinical data; the samples were de-identified and VCF positions have been randomized to prevent downstream identification. As a result of randomization, the sample VCF reference calls at a specific position don’t always match the base calls from a reference sequence.

    Along with the inputs, the example dierctory contains output from each Jacquard command, as explained below.


  1. Create an output directory.

  1. The translate command creates new VCFs, adding a controlled vocabulary of new FORMAT tags.

    $ jacquard translate examples/00-input_vcfs/ <output_dir>

  1. The merge command integrates a directory of VCFs into a single VCF.

    $ jacquard merge examples/01-translated/ <output_vcf_file>

  1. The summarize command adds new INFO fields and FORMAT tags that combine variant data from the merged VCF.

    $ jacquard summarize examples/02-merged.vcf <output_vcf_file>

  1. The expand command explodes a VCF file into a tab-delimited file.

    $ jacquard expand examples/03-summarized.vcf <output_tsv_file>

Refer to Overview for more information on Jacquard.