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Import FASTQ Files

Use the command-line interface to load FASTQ data into your cases. For information about setting up the tool, see Command-Line Interface.

ClosedStage and Link FASTQ Files

Staging files allows you to upload FASTQ data before the sample ID is created, and then link files to cases after the sample ID becomes available. The files remain in the staging directory and can be reused for future cases. To attach a FASTQ to a single sample, see Upload FASTQ Files to a Case.

1. Create or locate a directory of files you intend to upload. The directory must meet the following requirements:
• The directory contains FASTQ files for a single sample only.
• The FASTQ files have matching read 1 and read 2 files, identified by _R1 or _R2 in the filename.
• The FASTQ files have the appropriate *.fastq.gz or *.fq.gz extension. Files without this extension are ignored.
2. Use the stage command to create the directory and add files.

$ java -jar wgs-cli-<version>.jar --configFilePath <configfilepath> stage --stageDirectory <stage directory path> --localDirectory <local directory path>

Where:

• local directory path is the path to the local FASTQ folder.
• configfilepath is the path for the configuration file. If no path is specified, <HOME>/.illumina/uploader-config.json is used.
• stage directory path is the path to the remote stage directory.

Example:

java -jar wgs-cli.jar --configFilePath cliConfig/customConfig.json stage --stageDirectory stagefiles --localDirectory Documents/sampledata/sample123

3. Create a new case and assign a test that uses the Variant Analysis - From FASTQ pipeline.
4. For each subject in the case, do as follows.
  1. Select Link FASTQ data.
  2. In the FASTQ Files field, enter the location of the staged file directory (eg, stagefiles).
  3. In the Sample ID field, enter the sample name.
5. Select Submit.
ClosedUpload FASTQ Files to a Case

When you upload a FASTQ file directly to a case, you directly link the file to a sample in the case. To upload FASTQ files that can be used for more than one case, see Stage and Link FASTQ Files.

1. Use the fastqs command to upload and associate the files with a sample.

java -jar wgs-cli.jar --configFilePath <configfilepath> fastqs --localDirectory <local directory path> --sampleId <sample id>

Where:

• local directory path is the path to the local FASTQ folder.
• configfilepath is the path for the configuration file. If no path is specified, <HOME>/.illumina/uploader-config.json is used.
• sample id is the sample identifier used for the subject in the case.

Example:

java -jar wgs-cli-1.13.0.jar --configFilePath cliConfig/customConfig.json fastqs --localDirectory Documents/sampledata/sample123 --sampleId sample123

2. For each subject in the case, enter the sample name.
ClosedPreserving File Order for Other Analyses

For consistent results when analyzing the same file set using DRAGEN offline, input the files in the same order they were used by TruSight Software.

To view the file order, do as follows:

1. From the Subject Info page, select Analysis and then select the Files tab.
2. In the Structural Variants file section, select the *-joint-sv-replay.json file to download it.
3. Open the file in a text editor. The input files are listed in the command_line section at the top of the file.

Example:

--bam-input \/mount\/bams\/brotherX8RS4jFrGZQ.bam --bam-input \/mount\/bams\/father3azHzl3nhGc.bam --bam-input \/mount\/bams\/motherCugptwoyIDg.bam --bam-input \/mount\/bams\/proband0FWhv3R9fuU.bam