A Python program for evaluating site-level concordance of a query VCF against a truth VCF.
This tool compares two variant callsets against each other and produces a CSV file with summary metrics. The summary metric CSV file contains:
- Variant type: SNV or INDEL
- Total number of variants in the truth and query VCF files
- Total true-positive, false-positive, and false-negative calls
- Recall and Precision
python3 VCFCompare.py --truth truth.vcf --query query.vcf --output output