Enabling visualization for a VCF case

Loading local alignment files* to your case in Emedgene.

Visualization is automatically available for cases analyzed from FASTQ or BAM files. For cases analyzed only from VCF files, read alignment visualization can still be enabled by providing alignment files (BAM+BAI or CRAM+CRAI).

You can enable mapping visualization for a VCF case in three ways:

1. API-based case creation: Define the location of alignment files directly in the JSON payload.

2. Batch upload: Include the paths to visualization files in the input CSV when uploading cases in bulk.

3. Manual upload of local alignment files:

• Click the Load local file button on top of the Visualization section.

• Select relevant alignment files stored on your PC.

• Once uploaded, choose which samples to visualize by selecting their names from the top of the viewer.

Note:

Ensure that BAI or CRAI index files are uploaded alongside BAM or CRAM files for successful visualization.