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 built at Sat, 29 Jun 2024 20:47:29 -0400.
0 comments
Please sign in to leave a comment.