CNV Finding parameters

You can adjust Copy Number Variant (CNV) finding parameters to optimize your analysis results when you create or edit Ion Reporter™ Software analysis workflows.

IMPORTANT! Use the default parameter settings unless you are an advanced user.

Parameter Name

Description

Main tab

Analysis (applies to all CNV finding algorithms)

CNV Sensitivity

Sensitivity. Only when CUSTOM option is selected, the value of editable parameter Transition Penalty, available in Advanced tab in CNV parameters, will be utilized by the algorithm.

Allowed values: Low, Medium, High, or Custom

Suggested trial value: Medium

CNV Somatic

IMPORTANT! The somatic gene-level CNV calling parameter is for beta use only, and requires BED files and a copy number informatics baseline containing gene and pooling information. This parameter is not for use for germline copy number calling such as in ReproSeq workflows or other analysis workflows, which are designed to detect low pass whole genome aneuploidy events.

Allowed values: True or False

Suggested trial value: False

Advanced tab

Gender calling

CNV Gender Caller Enable Flag

Flag to indicate whether Gender caller should be invoked.

Allowed values: True or False

Suggested trial value: False

This flag is valid only for analysis workflows that are used to detect Low Pass whole genome aneuploidy events, such as Ion ReproSeq™ analysis workflows and other low pass whole genome analysis workflows that are used for aneuploidy research.

CNV Gender Threshold

Specifies threshold ratio of chrY to Autosomes for taking male/female call.

Allowed values: 0 to unlimited

Suggested trial value: 7

CNV Gender Min Mapping QV

Specifies min mapping qv of reads to consider in gender calling.

Allowed values: 0 to 255

Suggested trial value: 30

CNV Gender Min Autosomes Count

Specifies min number of required filtered reads in autosomes.

Allowed values: 0 to unlimited

Suggested trial value: 25,000

CNV CHRM to Autosomes Ratio Min Mapping QV

Specifies min mapping qv of reads to consider in calculating chrM A Ratio.

Allowed values: 0 to 255

Suggested trial value: 30

Sample Filtering (applies only to VCIB CNV finding algorithm)

Read Count

User to enter a threshold number (integer).

Allowed values: 10,000 to unlimited

Suggested trial value: 100,000

min-mapping-qv

Minimum mapping quality value required for a read to be counted.

Allowed values: 0 to unlimited

Suggested trial value: 0

Percent Non Zero Amplicons.

Percent of reads aligning to an amplicon in the target regions file.

User to enter a threshold number (integer).

Allowed values: 50 to 100

Suggested trial value: 60

MAPD threshold

Sample will fail if MAPD is above this threshold.

User to enter a threshold number (float).

Allowed values: 0 to unlimited

Suggested trial value: 0.5

Analysis (applies only to VCIB CNV finding algorithm)

NPC

Number of Principal Components used for correction.

Allowed values: 0 to 12

Suggested trial value: 4

CNV Shift Type

Methods of CNV shift: 'Median Amplicon' where median Copy Number of autosomal amplicons is set to 2; or 'Median Gene' where median Copy Number of the autosomal genes is set to 2; or 'VALUE_BASED_ON_MEDAMP' where the amount of subtraction in log2 ratio to the result of the CNV Shift method used; or 'MAXGENE' where the log2-normalized counts for each gene in the panel is adjusted by first setting the median of the highest counts gene to the expected normal value (log2N=0) and maintaining the relative copy number of the two BRCA genes. MAXGENE ensures that at least one gene is normal copy number internally, minimizing FP calls due to slight differences in copy number between the genes in germline samples; or 'FLATGENE' where the log2normalized counts for each gene is adjusted by setting median of each gene to the expected normal value (log2N=0) independently of the other gene. FLATGENE ensures that both genes have normal copynumber internally, making calling germline exon deletion variants possible in somatic whole gene deletion samples.

Allowed values: MEDGENE, MEDAMP, VALUE_BASED_ON_MEDAMP, MAXGENE, or FLATGENE

Suggested trial value: MEDGENE

CNV Shift Value

The amount of subtraction in log2 ratio to the result of the CNV Shift method used. May be used to fix an error in the CNV Shift method. Shift Value is only used when the Shift Type is set to VALUE_BASED_ON_MEDAMP.

Allowed values: -2 to 2

Suggested trial value: 0

Analysis (applies only to aneuploidy analysis workflows) [1]

Enable Mosaicism Detection

Enable Mosaicism Detection

Allowed values: True or False

Suggested trial value: False

Enable Smoothing

Enable Smoothing

Allowed values: True or False

Suggested trial value: False

Set Tile Size for aneuploidy Workflow

Set the tile size for Ion ReproSeq™ analysis workflows, designed for use with aneuploidy research.

The tile size used for creating the aneuploidy baseline must match the tile size selected here.

Allowed values: 1 to 10,000,000

Suggested trial value: 2,000,000

Hide called gender

Hide gender called by CNV gender calling.

Allowed values: True or False

Suggested trial value: False

Analysis

Plot Y chromosome for Female or Unknown Gender?

Plot Y chromosome for Female or Unknown Gender.

Allowed values: True or False

Suggested trial value: False

Analysis (applies only to Exon Deletions)

Cutoff for non-integer CN calls

Specifies the cutoff for making CN #calls that are not precisely of integer values.

Allowed values: 0 to 0.50

Suggested trial value: 0.30

Max Calls

Specifies the number of non-contiguous exon variant calls above which the sample will fail QC.

Allowed values: 0 to 47

Suggested trial value: 4

Min Quality

Specifies the quality score below which a CNV variant is classified as a NOCALL.

Allowed values: 0 to 100

Suggested trial value: 10

Analysis (applies only to Liquid Biopsy and Ion AmpliSeq™ HD)

Minimum Tag Family Size

Minimum number of reads with the same tag required to form a functional family.

Allowed values: 0 to unlimited

Suggested trial value: 0

Max Fold Difference for Loss

Maximum fold difference relative to reference for calling a loss.

Allowed values: 0 to 1

Suggested trial value: 0.85

Min Fold Difference for Gain

Minimum fold difference relative to reference for calling a gain.

Allowed values: 1 to unlimited

Suggested trial value: 1.15

P-value for maximum calls

P-value for maximum calls.

Allowed values: 0 to 1

Suggested trial value: 0.00001

Analysis (applies to all CNV finding algorithm types except VCIB CNV algorithm)

CNV Transition Penalty

Transition Penalty dictates the likelihood that the algorithm will call a different ploidy state between two adjacent data points. Transition Penalty is logarithm (to the base 10) of Transitional Probability. Lower (more negative) values will make it less likely that the algorithm will call adjacent data points as ploidy states that are different from each other. The Transition Penalty parameter edited here will only take effect when using the CUSTOM CNV Sensitivity setting. When CNV MOSAICISM parameter is not enabled, the maximum value supported for Transition Penalty is -1.05. When CNV MOSAICISM parameter is enabled, the maximum value supported for Transition Penalty is -2.31.

Allowed values: -1,000,000 to -1.05

Suggested trial value: -8

Analysis (applies only to VCIB CNV finding algorithm when custom panel is focal amplication)

CNV Gain Threshold

Threshold value (greater than or equal to 0) for calling GAIN in autosomes

Allowed values: 0 to unlimited

Suggested trial value: 4

CNV Gain Threshold XY

Threshold value (greater than or equal to 0) for calling GAIN in X or Y for males.

Allowed values: 0 to unlimited

Suggested trial value: 3

Gain Confidence Level

Confidence level value (greater than 0 and less than 1) to be used to compare to gain-threshold or gain_threshold_xy.

Allowed values: 0 to 1

Suggested trial value: 0.05

Analysis (applies only to Hidden Gender aneuploidy analysis workflow) [2]

Male Normal Ploidy Lower Bound

Male Minimum Normal Ploidy for Hidden Gender aneuploidy analysis workflow.

Allowed values: 0 to 100,000

Suggested trial value: 0.8

Male Normal Ploidy Upper Bound

Male Maximum Normal Ploidy for Hidden Gender aneuploidy analysis workflow

Allowed values: 0 to 100,000

Suggested trial value: 1.2

Female Normal Ploidy Lower Bound

Female Minimum Normal Ploidy for Hidden Gender aneuploidy analysis workflow.

Allowed values: 0 to 100,000

Suggested trial value: 1.8

Female Normal Ploidy Upper Bound

Female Maximum Normal Ploidy for Hidden Gender aneuploidy analysis workflow

Allowed values: 0 to 100,000

Suggested trial value: 2.2

1 Currently, these parameters apply to the Ion ReproSeq™ PGS w1.1, Ion ReproSeq™ No Gender PGS w1.1, and Ion ReproSeq™ Mosaic PGS w1.1. analysis workflows.
2 Currently, these paramaters apply only to the Ion ReproSeq™ No Gender PGS w1.1 analysis workflow.