search

NBISweden / ejprd

1 stars 0 forks source link

Add VCF files to the gdi-starter-kit configuration with a visualisation in a Jupyter notebook #15

Open wna-se opened 2 months ago

wna-se commented 2 months ago

It would be useful to start exploring data that is close to use case as we configure the different GDI Starter Kit services. A possible solution could be to load VCF files in addition to or instead of the BAM files referenced in the default configuration and set up a Jupyter notebook to run queries on the GDI services (on the secure network).

wna-se commented 2 months ago

Replicate IGV-session from Rackham

  1. Starting Integrative Genomics Viewer (IGV) on Rackham/Snowy
  2. Open $PROJECT_DIR/private/data/processed_data/region_vcfs/Case1_IC.reg.vcf.gz
  3. Navigate to chr19:39,021,117-39,104,472

Example