CNV Finding parameters

You can adjust Copy Number Variant (CNV) finding parameters to optimize 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 (apply only to Anueploidy analysis workflows)
CNV Sensitivity	Sensitivity. The value of editable parameter Transition Penalty is used by the algorithm only when CUSTOM option is selected, This option is available in Advanced tab for CNV parameters. Allowed values: Low, Medium, High, or Custom
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
Advanced tab
Gender calling
CNV Gender Caller Enable Flag	Flag to indicate whether Gender caller should be invoked. Allowed values: True or 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
CNV Gender Min Mapping QV	Specifies minimum mapping qv of reads to consider in gender calling. Allowed values: 0 to 255
CNV Gender Min Autosomes Count	Specifies minimum number of required filtered reads in autosomes. Allowed values: 0 to unlimited
CNV CHRM to Autosomes Ratio Min Mapping QV	Specifies minimum mapping qv of reads to consider in calculating chrM A Ratio. Allowed values: 0 to 255
Sample Filtering (applies only to VCIB CNV finding algorithm)
Read Count	User to enter a threshold number (integer). Allowed values: 10,000 to unlimited
min-mapping-qv	Minimum mapping quality value required for a read to be counted. Allowed values: 0 to unlimited
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
MAPD threshold Sample will fail if MAPD is above this threshold.	User to enter a threshold number (float). Allowed values: 0 to unlimited
Analysis (applies only to VCIB CNV finding algorithm)
NPC	Number of Principal Components used for correction. Allowed values: 0 to 12
CNV Shift Type	Allowed values: MEDGENE, MEDAMP, VALUE_BASED_ON_MEDAMP, MAXGENE, or FLATGENE. The following CNV shift methods are available. Median Amplicon – The median copy number of autosomal amplicons is set to 2. Median Gene – The median copy number of autosomal genes is set to 2. VALUE_BASED_ON_MEDAMP – The subtraction value applied to the log2 ratio is based on the result of the CNV shift method used. MAXGENE – The log2-normalized counts for each gene in the panel are adjusted by first setting the median of the gene with the highest counts to the expected normal value (log2N = 0), while maintaining the relative copy number of the two BRCA genes. This method assumes that at least one gene has a normal copy number internally, which can reduce false-positive calls caused by small copy-number differences between genes in germline samples. FLATGENE – The log2-normalized counts for each gene are adjusted by independently setting the median of each gene to the expected normal value (log2N = 0). This method assumes that both genes have a normal internal copy number, enabling detection of germline exon deletion variants in somatic whole-gene deletion samples.
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
Tumor Cellularity Selection	Select a value to use tumor calculated tumor fraction or user-specified Percent Tumor Cellularity in sample. Allowed values: Manually input Tumor Cellularity input per user or Auto-calculated tumor cellularity. The minimum amount that cellularity can be adjusted is 40%, for both auto-calculated and manual input tumor cellularity.
Analysis (applies only to aneuploidy analysis workflows) ^[1]
Enable Mosaicism Detection	Enable Mosaicism Detection Allowed values: True or False
Enable Smoothing	Enable Smoothing Allowed values: True or 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
Hide called gender	Hide gender called by CNV gender calling. Allowed values: True or False
Analysis
Plot Y chromosome for Female or Unknown Gender?	Plot Y chromosome for Female or Unknown Gender. Allowed values: True or 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
Max Calls	Specifies the number of non-contiguous exon variant calls above which the sample will fail QC. Allowed values: 0 to 47
Min Quality	Specifies the quality score below which a CNV variant is classified as a NOCALL. Allowed values: 0 to 100
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
Max Fold Difference for Loss	Maximum fold difference relative to reference for calling a loss. Allowed values: 0 to 1
Min Fold Difference for Gain	Minimum fold difference relative to reference for calling a gain. Allowed values: 1 to unlimited
P-value for maximum calls	P value for maximum calls. Allowed values: 0 to 1
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
Analysis (applies only to VCIB CNV finding algorithm when custom panel is focal amplification)
CNV Gain Threshold	Threshold value (≥0) for calling GAIN in autosomes Allowed values: 0 to unlimited
CNV Gain Threshold XY	Threshold value (≥0) for calling GAIN in X or Y for males. Allowed values: 0 to unlimited
Gain Confidence Level	Confidence level value (>0 and <1) to be used to compare to gain-threshold or gain_threshold_xy. Allowed values: 0 to 1
Analysis (applies only to Hidden Gender aneuploidy analysis workflow) ^[2] These settings apply only to aneuploidy workflows which provide only information whether the sex chromosomes look Normal or Abnormal, based on what is expected for the Expected Normal Ploidy of sex chromosomes on a normal XX female or a normal XY male.
Male Normal Ploidy Lower Bound	Male Minimum Normal Ploidy for Hidden Gender aneuploidy analysis workflow. Allowed values: 0 to 100,000
Male Normal Ploidy Upper Bound	Male Maximum Normal Ploidy for Hidden Gender aneuploidy analysis workflow Allowed values: 0 to 100,000
Female Normal Ploidy Lower Bound	Female Minimum Normal Ploidy for Hidden Gender aneuploidy analysis workflow. Allowed values: 0 to 100,000
Female Normal Ploidy Upper Bound	Female Maximum Normal Ploidy for Hidden Gender aneuploidy analysis workflow Allowed values: 0 to 100,000

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 parameters apply only to the Ion ReproSeq™ No Gender PGS w1.1 analysis workflow.