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READVIZ_SETUP.md

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If you have alignment files in .bam or .cram format for the sample(s) in your VCF, seqr allows read data for individual variants to be viewed in the browser using IGV.js.

If your read files are located on the machine that's running the seqr application server, these steps will enable viewing this read data through IGV.js:

  1. When running seqr using docker-compose (as described here), place the bam/cram and index files in the ./data/readviz/ sub-directory that was created under the directory containing the docker-compose.yml file. When you start seqr, docker-compose will mount the ./data/readviz/ directory to a /readviz top-level directory inside the seqr container.

If running seqr using the seqr-helm charts, place the bam/cram and index files inside /var/seqr/seqr-static-media.

  1. Create a tab-delimited or comma-delimited text file - let's call it bam_paths.tsv - with these 2 columns (and no header line):

    individual_id - the seqr individual id

    bam_or_cram_path - the absolute path of the .bam or .cram file on the local filesystem where the seqr gunicorn server is running (eg. /readviz/dir/file.bam). Each bam/cram file must also have an index file next to it (.bam.bai or .cam.crai).

  2. Go to the project page in seqr and click "Edit Datasets" and then click on the "Add BAM/CRAM Paths" tab in the resulting pop up. Upload the file from step 1 and click the "Submit" button