Mirror of Marxist-Leninist/mva-hackathon-2026 incl. genome-wide addendum, dosage model, contraindications
4533472 verified | #!/usr/bin/env python3 | |
| """Extract BUB1B-region candidate variants from the challenge VCF. | |
| Usage: python3 extract_candidates.py /path/to/WGS.vcf.gz | |
| Requires: bcftools. Outputs candidate table with GT/AD/DP/GQ. | |
| No patient data is embedded in this script. | |
| """ | |
| import subprocess, sys | |
| VCF = sys.argv[1] | |
| REGION = '15:40161068-40221122' # BUB1B, GRCh38, numeric contigs (no chr prefix in this VCF) | |
| out = subprocess.run(['bcftools','view','-H',VCF,REGION],capture_output=True,text=True).stdout | |
| for line in out.splitlines(): | |
| f = line.split('\t') | |
| fmt = f[8].split(':'); s = dict(zip(fmt, f[9].split(':'))) | |
| print(f[1], f[3]+'>'+f[4], f[6], 'GT='+s.get('GT','.'), 'AD='+s.get('AD','.'), 'DP='+s.get('DP','.'), 'GQ='+s.get('GQ','.')) | |