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 |
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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. |
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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. |
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Flag to indicate whether Gender caller should be invoked. 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. |
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Specifies threshold ratio of chrY to Autosomes for taking male/female call. |
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Specifies min mapping qv of reads to consider in gender calling. |
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Specifies min number of required filtered reads in autosomes. |
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Specifies min mapping qv of reads to consider in calculating chrM A Ratio. |
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Sample Filtering (applies only to VCIB CNV finding algorithm) |
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User to enter a threshold number (integer). |
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Minimum mapping quality value required for a read to be counted.
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Percent of reads aligning to an amplicon in the target regions file. |
User to enter a threshold number (integer). |
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Sample will fail if MAPD is above this threshold. |
User to enter a threshold number (float). |
Number of Principal Components used for correction. |
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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 copy number 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 |
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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. |
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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 |
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Analysis (applies only to aneuploidy analysis workflows) [1] |
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Enable Mosaicism Detection |
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Enable Smoothing |
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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. |
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Hide gender called by CNV gender calling. |
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Plot Y chromosome for Female or Unknown Gender. |
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Specifies the cutoff for making CN #calls that are not precisely of integer values. |
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Specifies the number of non-contiguous exon variant calls above which the sample will fail QC. |
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Specifies the quality score below which a CNV variant is classified as a NOCALL. |
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Analysis (applies only to Liquid Biopsy and Ion AmpliSeq™ HD) |
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Minimum number of reads with the same tag required to form a functional family. |
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Maximum fold difference relative to reference for calling a loss. |
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Minimum fold difference relative to reference for calling a gain. |
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P-value for maximum calls. |
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Analysis (applies to all CNV finding algorithm types except VCIB CNV algorithm) |
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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. |
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Analysis (applies only to VCIB CNV finding algorithm when custom panel is focal amplification) |
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Threshold value (greater than or equal to 0) for calling GAIN in autosomes |
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Threshold value (greater than or equal to 0) for calling GAIN in X or Y for males. |
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Confidence level value (greater than 0 and less than 1) to be used to compare to gain-threshold or gain_threshold_xy. |
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Analysis (applies only to Hidden Gender aneuploidy analysis workflow) [2] |
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Male Minimum Normal Ploidy for Hidden Gender aneuploidy analysis workflow. |
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Male Maximum Normal Ploidy for Hidden Gender aneuploidy analysis workflow |
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Female Minimum Normal Ploidy for Hidden Gender aneuploidy analysis workflow. |
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Female Maximum Normal Ploidy for Hidden Gender aneuploidy analysis workflow |
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