Example Commands for Processing FASTQ Data

After you have loaded your reference, you can process input FASTQ data. Choose the example that best matches your data sets. These commands can take up to approximately 30 minutes to run on a 24 core server with SSD drives on a 30x coverage whole human genome when running end-to-end (FASTQ input to VCF output). The speed scales with input size, so a 60x coverage genome would take twice as long. Exome data takes a fraction of the time. A successful result is indicated by the following message (an application exit code of 0 when run from a script):

DRAGEN finished normally

This message is followed by a block of metrics such as read count and performance. If there is a problem with the command line options, an error is displayed, followed by help usage. You may need to scroll up to see the error.

The DRAGEN log can be redirected to a file, to keep the record for future reference.

To get help on dragen command line options, run the following command:

dragen -h

The example commands shown in this document are formatted for visual display and include line feed characters. To avoid copy-paste errors, each example command is contained in an individual shell script in /opt/edico/examples/. These examples have the following requirements:

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All commands accept either FASTQ or gzipped FASTQ (fastq.gz). DRAGEN automatically determines the file type.

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All commands include the -f option, which forces the output file to be overwritten if it exists.

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All commands assume that your DRAGEN reference (hash table) directory is /staging/human/reference/hg19/hg19.fa.k_21.f_16.m_149, and your FASTA reference file is /staging/human/reference/hg19/hg19.fa. Replace those with the correct references or directory paths, if needed.

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All command examples assume that the example data package is in /staging/examples (in particular, the .fastq and fastq.gz files are expected to be in /staging/examples/reads).

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To run these example commands, you must have write access to the /staging/examples folder.