CNV Caller Options

cnv-blacklist-bed

Regions to blacklist for CNV processing.

--cnv-blacklist-bed

cnv-cbs-alpha

Significance level for the test to accept change points. Default is 0.01.

--cnv-cbs-alpha

cnv-cbs-eta

Type I error rate of the sequential boundary for early stopping when using the permutation method. Default is 0.05.

--cnv-cbs-eta

cnv-cbs-kmax

Maximum width of smaller segment for permutation. Default is 25.

--cnv-cbs-kmax

cnv-cbs-min-width

Minimum number of markers for a changed segment. Default is 2.

--cnv-cbs-min-width

cnv-cbs-nmin

Minimum length of data for maximum statistic approximation. Default is 200.

--cnv-cbs-nmin

cnv-cbs-nperm

Number of permutations used for p-value computation. Default is 10000.

--cnv-cbs-nperm

cnv-cbs-trim

Proportion of data to be trimmed for variance calculations. Default is 0.025.

--cnv-cbs-trim

cnv-counts-method

Overlap method for counting alignment.

--cnv-counts-method

cnv-enable-gcbias-correction

Controls GC bias correction.

--cnv-enable-gcbias-correction

cnv-enable-gcbias-smoothing

Controls smoothing of the GC bias correction across adjacent GC bins with an exponential kernel. Default is true.

--cnv-enable-gcbias-smoothing

cnv-enable-plots

Enable/disable generation of plots. Default is false.

--cnv-enable-plots

cnv-enable-ref-calls

When true, copy neutral (REF) calls are included in the output VCF.

--cnv-enable-ref-calls

cnv-enable-self-normalization

Enable/disable self-normalization.

--cnv-enable-self-normalization

cnv-enable-tracks

Enable/disable generation of track files that can be imported into IGV for viewing. Default is true.

--cnv-enable-tracks

cnv-extreme-percentile

Extreme median percentile value at which to filter out samples. Default is 2.5.

--cnv-extreme-percentile

cnv-filter-bin-support-ratio

Filters out a candidate event if the span of supporting bins is less than the specified ratio with respect to the overall event length. The default ratio is 0.2 (20% support).

--cnv-filter-bin-support-ratio

cnv-filter-copy-ratio

Minimum copy ratio threshold value centered about 1.0 at which a reported event is marked as PASS in the output VCF file. Default is 0.2

--cnv-filter-copy-ratio

cnv-filter-de-novo-quality

Phred-scale threshold for calling an event as de novo in the proband.

--cnv-filter-de-novo-quality

cnv-filter-length

Minimum event length in bases at which a reported event is marked as PASS in the output VCF file. Default is 10000.

--cnv-filter-length

cnv-filter-qual

The QUAL value at which a reported event is marked as PASS in the output VCF file.

--cnv-filter-qual

cnv-input

CNV input file instead of a BAM. Either target.counts.gz or tn.tsv.gz (for de novo).

--cnv-input

cnv-interval-width

Width of the sampling interval for CNV WGS processing.

--cnv-wgs-interval-width

cnv-matched-normal

Target counts file of the matched normal sample.

--cnv-matched-normal

cnv-max-percent-zero-samples

Threshold for filtering out targets with too many zero coverage samples. Default is 5%.

--cnv-max-percent-zero-samples

cnv-max-percent-zero-targets

Threshold for filtering out samples with too many zero coverage targets. Default is 5%.

--cnv-max-percent-zero-targets

cnv-merge-distance

Maximum segment gap allowed for merging segments.

--cnv-merge-distance

cnv-merge-threshold

The maximum segment mean difference at which two adjacent segments should be merged. The segment mean is represented as a linear copy ratio value.

--cnv-merge-threshold

cnv-min-mapq

Minimum MAPQ for alignment to be counted.

--cnv-min-mapq

cnv-normals-file

A single file to be used in the panel of normals. Can be specified multiple times, once for each file.

--cnv-normals-file

cnv-normals-list

A panel of normals file.

--cnv-normals-list

cnv-num-gc-bins

Number of bins for GC bias correction. Each bin represents the GC content percentage. Default is 25.

--cnv-num-gc-bins

cnv-ploidy

The normal ploidy value. Used for estimation of the copy number value emitted in the output VCF file. Default is 2.

--cnv-ploidy

cnv-qual-length-scale

Bias weighting factor to adjust QUAL estimates for segments with longer lengths. Advanced option that should not have to be modified. Default is 0.9303 (2-0.1).

--cnv-qual-length-scale

cnv-qual-noise-scale

Bias weighting factor to adjust QUAL estimates based on sample variance. Advanced option that should not have to be modified. Default is 1.0.

--cnv-qual-noise-scale

cnv-segmentation-mode

Segmentation algorithm to perform.

--cnv-segmentation-mode

cnv-skip-contig-list

A comma-separated list of contig identifiers to skip when generating intervals for WGS analysis. The default contigs that are skipped, if not specified, are "chrM,MT,m,chrm".

--cnv-wgs-skip-contig-list

cnv-slm-eta

Baseline probability that the mean process changes its value. Default is 1e-5.

--cnv-slm-eta

cnv-slm-fw

Minimum number of data points for a CNV to be emitted. Default is 0.

--cnv-slm-fw

cnv-slm-omega

Scaling parameter modulating relative weight between experimental/biological variance. Default is 0.3.

--cnv-slm-omega

cnv-slm-stepeta

Distance normalization parameter. The default value is 10000. Only valid for “HSLM”.

--cnv-slm-stepeta

cnv-target-bed

A properly formatted BED file that specifies the target intervals to sample coverage over. For use in WES analysis.

--cnv-target-bed

cnv-target-factor-threshold

Percentile of panel-of-normals medians used to filter out targets. The default value is 1% for whole genome processing and 10% for targeted sequencing processing.

--cnv-target-factor-threshold

cnv-truncate-threshold

Extreme outliers are truncated based on this percent threshold. Default is 0.1%.

--cnv-truncate-threshold