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, Project VCF, and VCF.

FASTQ

Use this option if you want the platform to perform secondary analysis and variant calling.

Accepted file types:

• .fastq.gz

• .fq.gz

• .bam

• .cram. Make sure you understand the current limitation for using CRAM files by expanding the section below.

Current limitation: CRAM input and reference compatibility

Context

Emedgene uses a specific genome reference assembly file (for example, hg38-alt_masked.cnv.graph.hla.rna-10-r4.0-1.tar.gz) for each DRAGEN version + genome reference (GRCh38 or GRCh37) combination. Both DRAGEN version and genome reference are configured per organization in Workbench & Pipeline settings.

Key requirement

When using CRAM files as input (instead of BAM), the same genome reference assembly file must be used during:

• The mapping/alignment stage (which produces the CRAM file)

• The variant calling stage (Emedgene secondary pipeline)

A mismatch in reference genome assembly files prevents the system from decompressing the CRAM file, leading to case analysis failure.

Best practices

• Confirm reference compatibility with your organization settings before launching a run

• If you receive CRAM files from an external lab, verify the specific reference genome file used to generate them

• If the reference is unknown or incompatible, convert CRAM → BAM and upload the BAM file instead

Project VCF

Use when working with a joint VCF file containing multiple samples.

Accepted file types:

• .pvcf

• .vcf

• .pvcf.gz

• .vcf.gz

Make sure the proband sample is listed first to ensure correct downstream calculations.

VCF

Use for cases where variants have already been called externally, or for cytogenetic array inputs.

Accepted file types:

• .vcf

• .vcf.gz

• .targeted.json

• .gt_sample_summary.json (v37.0+, DRAGEN Array v1.2+)

• .annotated_cyto.json (v100.39.0+, DRAGEN Array v1.3+)

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.

• 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.

• For large files (BAM/CRAM/FASTQ), browser upload is not recommended. Use Batch Upload, CLI, or cloud-to-cloud transfer instead to avoid incomplete or truncated uploads.