Metrics
Category Metrics
Overview
A collection of metrics relating to snps and indels within a variant-calling file (VCF).This table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| TOTAL_SNPS | The number of passing bi-allelic SNPs calls (i.e. non-reference genotypes) that were examined |
| NUM_IN_DB_SNP | The number of passing bi-allelic SNPs found in dbSNP |
| NOVEL_SNPS | The number of passing bi-allelic SNPS called that were not found in dbSNP |
| FILTERED_SNPS | The number of SNPs that are filtered |
| PCT_DBSNP | The fraction of passing bi-allelic SNPs in dbSNP |
| DBSNP_TITV | The Transition/Transversion ratio of the passing bi-allelic SNP calls made at dbSNP sites |
| NOVEL_TITV | The Transition/Transversion ratio of the passing bi-allelic SNP calls made at non-dbSNP sites |
| TOTAL_INDELS | The number of passing indel calls that were examined |
| NOVEL_INDELS | The number of passing indels called that were not found in dbSNP |
| FILTERED_INDELS | The number of indels that are filtered |
| PCT_DBSNP_INDELS | The fraction of passing indels in dbSNP |
| NUM_IN_DB_SNP_INDELS | The number of passing indels found in dbSNP |
| DBSNP_INS_DEL_RATIO | The Insertion/Deletion ratio of the indel calls made at dbSNP sites |
| NOVEL_INS_DEL_RATIO | The Insertion/Deletion ratio of the indel calls made at non-dbSNP sites |
| TOTAL_MULTIALLELIC_SNPS | The number of passing multi-allelic SNP calls that were examined |
| NUM_IN_DB_SNP_MULTIALLELIC | The number of passing multi-allelic SNPs found in dbSNP |
| TOTAL_COMPLEX_INDELS | The number of passing complex indel calls that were examined |
| NUM_IN_DB_SNP_COMPLEX_INDELS | The number of passing complex indels found in dbSNP |
| SNP_REFERENCE_BIAS | The rate at which reference bases are observed at ref/alt heterozygous SNP sites. |
| NUM_SINGLETONS | For summary metrics, the number of variants that appear in only one sample. For detail metrics, the number of variants that appear only in the current sample. |
GATK version 4.5.0.0 built at Tue, 9 Jan 2024 14:37:17 -0500.
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