Comparing Variant Caller Outputs

For lightweight VCF concordance:

pipeconcord compare caller_a.vcf caller_b.vcf --type vcf

The VCF comparator reports:

• normalized allele-level variant Jaccard
• sample overlap
• allele-specific genotype concordance
• allele-frequency correlation
• Ti/Tv ratio similarity

The built-in normalization splits multiallelic ALT records and trims shared prefix/suffix bases. It does not do reference-based left alignment. Normalize complex indels upstream when representation differences should not count as discordance.

For truth-set benchmarking, use specialized tools such as hap.py or vcfeval; pipeconcord is intended for pipeline regression and broad semantic comparison.