step1-fetch-clinvar-data.md

Manual curation, part I, technical: fetch the latest ClinVar data, attempt automatic mapping, extract unmapped traits

Run the automated protocol

Before running, set up the environment (Open Targets batches only):

• Common environment
• Protocol-specific environment

# Create directories for data processing
mkdir -p ${CURATION_RELEASE_ROOT}
cd ${CURATION_RELEASE_ROOT}

# Run the nextflow pipeline, resuming execution of previous attempt if possible.
nextflow run ${CODE_ROOT}/pipelines/generate_curation_spreadsheet.nf \
  --curation_root ${CURATION_RELEASE_ROOT} \
  -resume

Create a Google spreadsheet for curation

Duplicate a template. Paste the contents of ${CURATION_RELEASE_ROOT}/google_sheets_table.tsv file into it, starting with column H “ClinVar label”. Example of a table fully populated with data can be found here.