To load optional test sample files
Optionally, when you are building a model, you can load test sample files, which are positive controls (known aneuploidy) to estimate the sensitivity and specificity of the model. If you decide to load test sample files, no minimum number is required. The test samples can be raw data files (*.fasta, *.fastq, or *.fq) or aligned files (*.bam files). If the files are BAM files, then they must be aligned to a Build 37 reference. Optionally, you can also group the test samples. For example, you might have two files that are the same sample, such as R1 and R2, or you might have multiple lanes from the same sample, such as LZ001 and LZ002. When you group test samples, the same modeling variables (target chromosomes, NCV cutoffs, and so on) are applied to all the samples in the group. After you run the model, you can view the results of the NCVs calculations for your test samples to determine if the default NCV cutoff values are satisfactory, or if you should modify the values.
1. Click Test Samples.
The Load Test Samples dialog box opens. The targeted chromosomes are displayed next to dropdown lists at the bottom of the dialog box. For example, if chromosomes 13, 18, and 21 were selected as the targeted chromosomes on the Model page, then three dropdown lists are displayed – one for chromosome 13, one for chromosome 18, and one for chromosome 21. A Sex Chromosomes dropdown list is also displayed.
2. For the targeted chromosomes, indicate the target values – Undetermined, Normal, Trisomy, or Monosomy.
3. Do the following in the Load Test Samples dialog box:
a. Click Add to open the Open dialog box.
b. In the Open dialog box, browse to and select the appropriate test sample files.
c. Click Open to load the selected files into the Load Test Samples dialog box.
The Open dialog box closes. The Load Test Samples dialog box displays all the test files that were loaded as well as information about the loaded files – Normal indicator, Undetermined or the sex chromosomes that are being tested, if applicable, and the data status (Raw or Aligned).
4. Do one of the following in the Load Test Samples dialog box:
Option | Description |
|---|
To load and run the test sample files as-is | 1. Click OK. The Load Test Controls dialog box closes and all the test sample files are loaded and displayed in the Samples pane at the bottom of the Model page. |
To manually group the test sample files before running | |
To automatically group the test sample files before running | |