Visualize Data in IGV

This page provides instructions for visualizing DRAGEN secondary analysis outputs using IGV.

IGV (Integrative Genomics Viewer) is an interactive desktop tool for visualizing and exploring genomic data—like BAM/CRAM alignments, variants (VCF), and annotation tracks—so you can quickly inspect regions of interest, assess read support, and validate findings.

DRAGEN Germline analysis for Illumina TruPat Genome generates standard output formats such as BAM/CRAM and VCF files that can be directly loaded into IGV for visualization and review. The key files useful for IGV visualizations are listed below:

• Phased BAM: <sample_name>/<sample_name>.bam

  • Index: <sample_name>/<sample_name>.bam.bai

• Phased small variant VCF: <sample_name>/<sample_name>.hard-filtered.gvcf.gz

  • Index: <sample_name>/<sample_name>.hard-filtered.gvcf.gz.tbi

• CNV VCF: <sample_name>/<sample_name>.cnv.vcf.gz

  • Index: <sample_name>/<sample_name>.cnv.vcf.gz.tbi

• SV VCF: <sample_name>/<sample_name>.sv.vcf.gz

  • Index: <sample_name>/<sample_name>.sv.vcf.gz.tbi

• Phase block GTF: <sample_name>/<sample_name>.phase_blocks.gtf.gz

• MRJD VCF: <sample_name>/<sample_name>.mrjd.hard-filtered.vcf.gz

• MRJD phased BAM: <sample_name>/<sample_name>.mrjd.phased.bam

• MRJD VCF in haplotype separated format: <sample_name>/mrjd_supporting_files/<sample_name>.mrjd.<paralog_name>.vcf.gz

• SAM file containing reference region alignments for MRJD: <sample_name>/mrjd_supporting_files/<sample_name>.mrjd.reference_region_alignments.sam

IGV supports both loading data from local files and streaming tracks directly from signed URLs for remote, secure access.

Option 1 — Download files locally from ICA, then open in IGV. You can download the DRAGEN output files from ICA onto your computer and load them into IGV as local tracks. This can be done either via the ICA CLI (e.g., using icav2 projectdata download <file_path>) or directly from the ICA web browser UI by clicking data and download.

Click [Download] to start downloading from browser

Next, click File → Load from File to load local files to IGV.

Option 2 — Stream files directly into IGV using signed URLs. If you prefer not to download large files locally, you can stream tracks straight into IGV using signed URLs. Generate signed URLs with:

icav2 projectdata downloadurl -o table <file_path>

where file_path can be found by right-clicking the data, and copy either Path or ID

Then copy the output URL(s) and paste them into IGV (File → Load from URL) to load the tracks remotely.

We recommend using the following IGV preference for alignment:

• Group by: HP

• Color by: PS

• Display mode: squished

• Show softclips

• Turn off downsampling

Phased VCF, and Haplotagged BAM at TP53 Gene

In view above, reads are grouped by haplotype ("HP") and colored by Phase Block ("PS"). The grey reads are unphased, meaning they cannot be confidently assigned to either group.