Metrics
Category Metrics
Overview
This table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| NUM_ASSAYS |
The total number of assays (SNP and indels) in the VCF |
| NUM_NON_FILTERED_ASSAYS |
The total number of NON-filtered assays in the VCF |
| NUM_FILTERED_ASSAYS |
The total number of filtered assays in the VCF |
| NUM_ZEROED_OUT_ASSAYS |
The total number of zeroed-out (filtered out by Illumina in chip design) assays in the VCF |
| NUM_SNPS |
The number of bi-allelic SNP calls |
| NUM_INDELS |
The number of indel calls |
| NUM_CALLS |
The number of passing calls |
| NUM_AUTOCALL_CALLS |
The number of passing autocall calls |
| NUM_NO_CALLS |
The number of no-calls |
| NUM_IN_DB_SNP |
The number of high confidence SNPs found in dbSNP |
| NOVEL_SNPS |
The number of high confidence SNPS called that were not found in dbSNP |
| PCT_DBSNP |
The fraction of high confidence SNPs in dbSNP |
| CALL_RATE |
The overall call rate |
| AUTOCALL_CALL_RATE |
The overall autocall call rate |
| 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 4.6.0.0-33-gdffedfb built at Wed, 23 Oct 2024 21:44:48 -0400.
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