gnomAD data

How to update/download gnomAD

VCF files

1. If not existing, create gnomAD subfolder in genotoscope_data:

   cd path2analysis_root/genotoscope_data

   mkdir gnomAD

2. create subfolder for used version (GenOtoScope currently uses v2.1 for GRCh37/hg19):

   cd gnomAD

   mkdir gnomAD_v2.1

3. download files from gnomAD downloads:

   cd gnomAD_v2.1

   wget https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.vcf.bgz

   wget https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.vcf.bgz.tbi

4. rename bgz to gz (to be able to use pyVCF library without errors):

   mv gnomad.exomes.r2.1.1.sites.1.vcf.bgz gnomad.exomes.r2.1.1.sites.4.vcf.gz

   mv gnomad.exomes.r2.1.1.sites.1.vcf.bgz.tbi gnomad.exomes.r2.1.1.sites.1.vcf.gz.tbi

pLoF variants

• Navigate to gnomAD downloads

• Select gnomAD version for GRCh37

• Make current directory the genotoscope_data subfolder with the respective version of gnomAD:

  cd /path2genotoscope_data/gnomAD/gnomAD_v2.1

• Download all pLoF variants:

  wget https://storage.googleapis.com/gcp-public-data--gnomad/papers/2019-flagship-lof/v1.0/gnomad.v2.1.1.all_lofs.txt.bgz