picard.analysis

Class CollectOxoGMetrics.CpcgMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.CollectOxoGMetrics.CpcgMetrics

Enclosing class:

CollectOxoGMetrics

public static final class CollectOxoGMetrics.CpcgMetrics
extends htsjdk.samtools.metrics.MetricBase

Metrics class for outputs.

Field Summary

Fields

Modifier and Type	Field and 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 cause
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.
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.
java.lang.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.
java.lang.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_BASES
double	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 observed
java.lang.String	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 and Description
CpcgMetrics()

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

equals, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

SAMPLE_ALIAS

public java.lang.String SAMPLE_ALIAS

The name of the sample being assayed.

LIBRARY

public java.lang.String LIBRARY

The name of the library being assayed.

CONTEXT

public java.lang.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.

Constructor Detail

CpcgMetrics

public CpcgMetrics()