Metrics
Category Metrics
Overview
A class to store information relevant for biological rate estimation @author Yossi FarjounThis table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| nSites |
The count of sites used. |
| nThreeAllelesSites |
The count of sites in which a third allele was found. |
| nTotalReads |
The total number of reads over the het sites. |
| nDuplicateSets |
The number of duplicate sets examined. |
| nExactlyTriple |
The number of sets of size exactly 3 found. |
| nExactlyDouble |
The number of sets of size exactly 2 found. |
| nReadsInBigSets |
The number of reads in duplicate of sizes greater than 3. |
| nDifferentAllelesBiDups |
The number of doubletons where the two reads had different bases in the locus. |
| nReferenceAllelesBiDups |
The number of doubletons where the two reads matched the reference. |
| nAlternateAllelesBiDups |
The number of doubletons where the two reads matched the alternate. |
| nDifferentAllelesTriDups |
The number of tripletons where at least one of the reads didn't match either allele of the het site. |
| nMismatchingAllelesBiDups |
The number of tripletons where the two reads had different bases in the locus. |
| nReferenceAllelesTriDups |
The number of tripletons where the two reads matched the reference. |
| nAlternateAllelesTriDups |
The number of tripletons where the two reads matched the alternate. |
| nMismatchingAllelesTriDups |
The number of tripletons where at least one of the reads didn't match either allele of the het site. |
| nReferenceReads |
The number of reference alleles in the reads. |
| nAlternateReads |
The number of alternate alleles in the reads. |
| nMismatchingUMIsInDiffBiDups |
The number of UMIs that are different within Bi-sets that come from different alleles. |
| nMatchingUMIsInDiffBiDups |
The number of UMIs that are match within Bi-sets that come from different alleles. |
| nMismatchingUMIsInSameBiDups |
The number of UMIs that are different within Bi-sets that come from the same alleles. |
| nMatchingUMIsInSameBiDups |
The number of UMIs that are match within Bi-sets that come from the same alleles. |
| nMismatchingUMIsInCoOrientedBiDups |
The number of bi-sets with mismatching UMIs and same orientation. |
| nMismatchingUMIsInContraOrientedBiDups |
The number of bi-sets with mismatching UMIs and opposite orientation. |
| nBadBarcodes |
The number of sets where the UMIs had poor quality bases and were not used for any comparisons. |
| nGoodBarcodes |
the number of sets where the UMIs had good quality bases and were used for any comparisons. |
| biSiteHeterogeneityRate |
the rate of heterogeneity within doubleton sets. |
| triSiteHeterogeneityRate |
the rate of heterogeneity within tripleton sets |
| biSiteHomogeneityRate |
the rate of homogeneity within doubleton sets. |
| triSiteHomogeneityRate |
the rate of homogeneity within tripleton sets. |
| independentReplicationRateFromBiDups |
|
| independentReplicationRateFromTriDups |
The biological duplication rate (as a fraction of the duplicates sets) calculated from tripleton sets. |
| pSameUmiInIndependentBiDup |
When the alleles are different, we know that this is a biological duplication, thus we expect nearly all the UMIs to be different (allowing for equality due to chance). So we expect this to be near 1. |
| pSameAlleleWhenMismatchingUmi |
When the UMIs mismatch, we expect about the same number of different alleles as the same (assuming that different UMI implies biological duplicate) thus, this value should be near 0.5 |
| independentReplicationRateFromUmi |
Given the UMIs one can estimate the rate of biological duplication directly, as this would be the rate of having different UMIs in all duplicate sets. This is only a good estimate if the assumptions hold, for example if pSameUmiInIndependentBiDup is near 1. |
| replicationRateFromReplicateSets |
An estimate of the duplication rate that is based on the duplicate sets we observed. |
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.