Metrics
Category Metrics
Overview
Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison. @author Tim FennellThis table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| READ_GROUP |
The sequencing read group from which sequence data was fingerprinted. |
| SAMPLE |
The name of the sample who's genotypes the sequence data was compared to. |
| SNP |
The name of a representative SNP within the haplotype that was compared. Will usually be the exact SNP that was genotyped externally. |
| SNP_ALLELES |
The possible alleles for the SNP. |
| CHROM |
The chromosome on which the SNP resides. |
| POSITION |
The position of the SNP on the chromosome. |
| EXPECTED_GENOTYPE |
The expected genotype of the sample at the SNP locus. |
| OBSERVED_GENOTYPE |
The most likely genotype given the observed evidence at the SNP locus in the sequencing data. |
| LOD |
The LOD score for OBSERVED_GENOTYPE vs. the next most likely genotype in the sequencing data. |
| OBS_A |
The number of observations of the first, or A, allele of the SNP in the sequencing data. |
| OBS_B |
The number of observations of the second, or B, allele of the SNP in the sequencing data. |
GATK version 4.6.0.0-33-gdffedfb built at Wed, 23 Oct 2024 21:44:48 -0400.
0 comments
Please sign in to leave a comment.