ClinVarEPReports

Python scripts to generate ClinGen Expert Panel reports from ClinVar FTP files.

About this project

ClinVar outputs a submission_summary.txt.gz file containing a list of all SCV submissions per variant to its FTP site. The scripts in this project use this file to generate the following files in the subdirectory ClinVarEPReports/Reports_MM-DD-YYYY:

EPReports.py - this script outputs an Excel file containing each variant in the submission_summary.txt file that an EP needs to update or review. The Excel contains a README with summary stats and 8 structured tabs as detailed below:

• #1. Alert: ClinVar variants with an LP/VUS Expert Panel SCV with a DateLastEvaluated > 2 years from the date of this file (may overlap with variants on Tabs 2, 3 and 4).
• #2. Alert: ClinVar variants with a P/LP Expert Panel SCV AND a newer VUS/LB/B non-EP SCV (with a DateLastEvaluated up to 1 year prior of EP DateLastEvaluated; medically-significant conflict).
• #3. Alert: ClinVar variants with a VUS Expert Panel SCV AND a newer P/LP non-EP SCV (with a DateLastEvaluated up to 1 year prior of EP DateLastEvaluated).
• #4. Alert: ClinVar variants with a VUS Expert Panel SCV AND a newer LB/B non-EP SCV (with a DateLastEvaluated up to 1 year prior of EP DateLastEvaluated).
• #5. Priority: ClinVar variants WITHOUT an Expert Panel SCV, but in a gene in scope for the EP, with at least one P/LP SCV and at least one VUS/LB/B SCV (medically-significant conflict).')
• #6. Priority: ClinVar variants WITHOUT an Expert Panel SCV, but in a gene in scope for the EP, with at least one VUS SCV and at least one LB/B SCV.
• #7. Priority: ClinVar variants WITHOUT an Expert Panel SCV, but in a gene in scope for the EP, with >=3 concordant VUS SCVs from different submitters.
• #8. Priority: ClinVar variants WITHOUT an Expert Panel SCV, but in a gene in scope for the EP, with at least one P/LP SCV from (at best) a no assertion criteria provided submitter.

EPReports.py also generates an EPReportsStats Excel file containing the summary variant counts for each EP.

How to run these scripts

All scripts are run as 'python3 filename.py'. All scripts use FTP to take the most recent ClinVar FTP files as input and to output the files with the date of the FTP submission_summary.txt.gz file appended:

• ftp.ncbi.nih.gov/pub/clinvar/tab_delimited/submission_summary.txt.gz
• ftp.ncbi.nih.gov/pub/clinvar/tab_delimited/variation_allele.txt.gz
• ftp.ncbi.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz

These ClinVar files are then removed when finished.