## htsjdk.samtools.metrics.StringHeader
# GenotypeConcordance TRUTH_VCF=in/CEUTrio-snps.vcf CALL_VCF=in/CEUTrio-snps.vcf OUTPUT=picard/concordance TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891    OUTPUT_VCF=false INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Sat Oct 24 21:43:46 HST 2026

## METRICS CLASS	picard.vcf.GenotypeConcordanceDetailMetrics
VARIANT_TYPE	TRUTH_SAMPLE	CALL_SAMPLE	TRUTH_STATE	CALL_STATE	COUNT	CONTINGENCY_VALUES
SNP	NA12878	NA12891	HOM_REF	HET_REF_VAR1	31	FP,TN
SNP	NA12878	NA12891	HET_REF_VAR1	HOM_REF	30	TN,FN
SNP	NA12878	NA12891	HET_REF_VAR1	HET_REF_VAR1	50	TP,TN
SNP	NA12878	NA12891	HET_REF_VAR1	HOM_VAR1	24	TP,FP
SNP	NA12878	NA12891	HOM_VAR1	HET_REF_VAR1	18	TP,FN
SNP	NA12878	NA12891	HOM_VAR1	HOM_VAR1	41	TP
SNP	NA12878	NA12891	VC_FILTERED	VC_FILTERED	49	EMPTY


