Package picard.analysis
Class CollectOxoGMetrics.CpcgMetrics
- java.lang.Object
-
- htsjdk.samtools.metrics.MetricBase
-
- picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
- Enclosing class:
- CollectOxoGMetrics
@DocumentedFeature(groupName="Metrics", summary="Metrics") public static final class CollectOxoGMetrics.CpcgMetrics extends htsjdk.samtools.metrics.MetricBase
Metrics class for outputs.
-
-
Field Summary
Fields Modifier and Type Field Description long
ALT_NONOXO_BASES
The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that rules out oxidation as the causelong
ALT_OXO_BASES
The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that is consistent with oxidative damage.long
C_REF_ALT_BASES
The number of alt (A/T) basecalls observed at sites where the genome reference == C.double
C_REF_OXO_ERROR_RATE
The rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there were no bias between sites with a C reference base vs.double
C_REF_OXO_Q
C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.long
C_REF_REF_BASES
The number of ref basecalls observed at sites where the genome reference == C.String
CONTEXT
The sequence context being reported on.long
G_REF_ALT_BASES
The number of alt (A/T) basecalls observed at sites where the genome reference == G.double
G_REF_OXO_ERROR_RATE
The rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there were no bias between sites with a C reference base vs.double
G_REF_OXO_Q
G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.long
G_REF_REF_BASES
The number of ref basecalls observed at sites where the genome reference == G.String
LIBRARY
The name of the library being assayed.double
OXIDATION_ERROR_RATE
The oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASESdouble
OXIDATION_Q
-10 * log10(OXIDATION_ERROR_RATE)long
REF_NONOXO_BASES
The number of reference alleles observed as C in read 1 and G in read 2.long
REF_OXO_BASES
The number of reference alleles observed as G in read 1 and C in read 2.long
REF_TOTAL_BASES
The total number of reference alleles observedString
SAMPLE_ALIAS
The name of the sample being assayed.long
TOTAL_BASES
The total number of basecalls observed at all sites.int
TOTAL_SITES
The total number of sites that had at least one base covering them.
-
Constructor Summary
Constructors Constructor Description CpcgMetrics()
-
-
-
Field Detail
-
SAMPLE_ALIAS
public String SAMPLE_ALIAS
The name of the sample being assayed.
-
LIBRARY
public String LIBRARY
The name of the library being assayed.
-
CONTEXT
public String CONTEXT
The sequence context being reported on.
-
TOTAL_SITES
public int TOTAL_SITES
The total number of sites that had at least one base covering them.
-
TOTAL_BASES
public long TOTAL_BASES
The total number of basecalls observed at all sites.
-
REF_NONOXO_BASES
public long REF_NONOXO_BASES
The number of reference alleles observed as C in read 1 and G in read 2.
-
REF_OXO_BASES
public long REF_OXO_BASES
The number of reference alleles observed as G in read 1 and C in read 2.
-
REF_TOTAL_BASES
public long REF_TOTAL_BASES
The total number of reference alleles observed
-
ALT_NONOXO_BASES
public long ALT_NONOXO_BASES
The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that rules out oxidation as the cause
-
ALT_OXO_BASES
public long ALT_OXO_BASES
The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that is consistent with oxidative damage.
-
OXIDATION_ERROR_RATE
public double OXIDATION_ERROR_RATE
The oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASES
-
OXIDATION_Q
public double OXIDATION_Q
-10 * log10(OXIDATION_ERROR_RATE)
-
C_REF_REF_BASES
public long C_REF_REF_BASES
The number of ref basecalls observed at sites where the genome reference == C.
-
G_REF_REF_BASES
public long G_REF_REF_BASES
The number of ref basecalls observed at sites where the genome reference == G.
-
C_REF_ALT_BASES
public long C_REF_ALT_BASES
The number of alt (A/T) basecalls observed at sites where the genome reference == C.
-
G_REF_ALT_BASES
public long G_REF_ALT_BASES
The number of alt (A/T) basecalls observed at sites where the genome reference == G.
-
C_REF_OXO_ERROR_RATE
public double C_REF_OXO_ERROR_RATE
The rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there were no bias between sites with a C reference base vs. a G reference base.
-
C_REF_OXO_Q
public double C_REF_OXO_Q
C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
-
G_REF_OXO_ERROR_RATE
public double G_REF_OXO_ERROR_RATE
The rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there were no bias between sites with a C reference base vs. a G reference base.
-
G_REF_OXO_Q
public double G_REF_OXO_Q
G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
-
-