Select sample type

When creating a new case, the first step is to select the sample input type. This determines how your data will be processed and which quality metrics will be available later in the analysis.

You can choose from the following supported formats:

• FASTQ Accepted file types: .fastq.gz, .fq.gz, .bam, .cram Use this option if you want the platform to perform secondary analysis and variant calling.

• Project VCF Accepted file types: .pvcf, .vcf, .vcf.gz, .pvcf.gz Use when working with a joint VCF file containing multiple samples.

• VCF Accepted file types: .vcf, .vcf.gz, .targeted.json, .gt_sample_summary.json, .annotated_cyto.json (v100.39.0+) Use for cases where variants have already been called externally, or for array inputs with accompanying JSON files.

• Array Supported with DRAGEN Array v1.2 VCF and quality files. Use this option for cytogenetic array cases. Array results can be visualized in Genome View and the IGV tab, and sample-level quality metrics are available under the Lab tab.

Tips:

• Choose the input type carefully — it cannot be changed after the case is created.

• For joint gVCF or project VCF inputs, make sure the proband sample is listed first to ensure correct downstream calculations.

• Keep file paths simple (avoid spaces, parentheses, or very long names >255 characters). This helps prevent errors during upload

Warning:

If files are incomplete or corrupted, the case may still be created but will fail during processing. Double-check your files before uploading.