Command Details

Jacquard is a suite of tools that can be either run in succession or individually; the typical workflow is to run:

• translate
• merge
• summarize
• expand

Translate and summarize commands are useful only for supported callers; merge and expand work for any VCFs. Each of these commands is described in detail in the following pages.

General usage

$ jacquard <SUBCOMMAND> [ARGUMENTS] [OPTIONS]

For help on a specific command:

$ jacquard <SUBCOMMAND> --help

• Jacquard first writes output files to a temporary directory and only copies the files upon successful completion of each subcommand.
• Error, warning, and info messages are written to console and log file. Debug messages are only written to the log file (unless –verbose specified).

Input File Conventions

• Jacquard assumes that the first element of the filename (up to the first dot) is a patient identifier. For example:

• patientA-113.mutect.vcf
• patientA-113.strelka.snv.vcf
• patientA-113.strelka.indel.vcf

This set of three files all have the same patient identifier (patientA-113). The tumor-normal sample pairs will be combined into a single pair of tumor-normals columns in the merged VCF. See merge for more details.

• To translate a specific VCF dialect, Jacquard determines the source variant caller based on the VCF metaheaders. For this reason it is essential that you preserve all metaheaders in the source VCF.
• For a specific source VCF, Jacquard automatically determines the tumor and normal samples based on the column header and the metaheaders.