Run ACLI

The requirements to run Array Analysis CLI v2.1 are as follows.

• Manifest file (*.bpm and *.csv)
• CN model file (*.dat) — required for CNV PGx analysis only
• Cluster file (*.egt)
• IDAT files

It is recommended that you use the cluster file and CN model file (for CNV PGx analysis) available on the Array Analysis CLI v2.1 support site.

Samples that were prepared together should be analyzed together. It is not recommended to combine batches prepared with different reagent lots into a single analysis due to possible batch effects.

For CNV PGx analysis, a batch size of 96 samples or more is recommended to remove batch effect, and a minimum of 24 samples is required to run analysis. For a successful analysis, 22 samples must pass QC.

For genotyping analysis, there is no sample minimum required to run analysis.

Use the following instructions to start analysis. Refer to Command Index for parameters for all commands. Command examples show analysis for a Mac or Linux system.

1. Open a command prompt (Windows) or terminal window (Mac or Linux) and navigate to the desired directory.
2. Use the genotype call command to call genotypes. In the following example, an IDAT folder containing IDAT files is used instead of a sample sheet containing paths to IDAT files.

~$ array-analysis-cli genotype call --bpm-manifest

/user/productfiles/manifest.bpm --cluster-file

/user/productfiles/clusterfile.egt –-idat-folder /user/IDATs –-output-folder /user/gtc

3. Use the genotype gtc-to-vcf command to create VCF files from the GTC files generated by the genotype call command. In the following example, a GTC folder containing generated GTC files is used instead of a sample sheet containing paths to genotype files.

~$ array-analysis-cli genotype gtc-to-vcf --bpm-manifest /user/productfiles/manifest.bpm --csv-manifest

/user/productfiles/manifest.csv --genome-fasta-file

/user/productfiles/genome.fasta --gtc-folder /user/gtc --output-folder /user/genotype-vcf

4. Use the copy-number call command to call CNVs. The example shows a GTC folder containing GTC files instead of a sample sheet.

~$ array-analysis-cli copy-number call --cn-model

/user/productfiles/cnmodel.dat --gtc-folder /user/gtc --output-folder /user/copynumber-vcf

5. [Optional] Use the copy-number train command to retrain the copy number model. The following example shows a GTC folder containing GTC files generated by the genotype call command instead of a sample sheet.

~$ array-analysis-cli copy-number train --bpm-manifest

/user/productfiles/manifest.bpm -–genome-fasta-file

/user/productfiles/genome.fasta –-gtc-folder /user/gtc –-output-folder /user/productfiles/cnmodelnew.dat

6. Navigate to the directory where the caller was installed.