Getting Started

1. Install Hail:

   pip install hail
   

2. Use hailctl to start a Google Dataproc cluster with the gnomad package installed (see Hail on the Cloud for more detail on hailctl):

   hailctl dataproc start cluster-name --packages gnomad
   

3. Connect to a Jupyter Notebook on the cluster:

   hailctl dataproc connect cluster-name notebook
   

4. Import gnomAD data in Hail Table format:

   • gnomAD v2.1.1 variants:

     from gnomad.resources.grch37 import gnomad
     
     gnomad_v2_exomes = gnomad.public_release("exomes")
     exomes_ht = gnomad_v2_exomes.ht()
     exomes_ht.describe()
     
     gnomad_v2_genomes = gnomad.public_release("genomes")
     genomes_ht = gnomad_v2_genomes.ht()
     genomes_ht.describe()
     

   • gnomAD v3 variants:

     from gnomad.resources.grch38 import gnomad
     gnomad_v3_genomes = gnomad.public_release("genomes")
     ht = gnomad_v3_genomes.ht()
     ht.describe()
     

5. Shut down the cluster when finished with it:

   hailctl dataproc stop cluster-name