Path to normal WIG file. Default: [%default]

Path to mappability score WIG file. Default: [%default]

Median corrected depth from panel of normals. Default: [%default]

Path to bed file containing exon regions. Default: [%default]

File containing Centromere locations; if not provided then will use hg19 version from ichorCNA package. Default: [%default]

Length of region flanking centromere to remove. Default: [%default]

Initial normal contamination; can be more than one value if additional normal initializations are desired. Default: [%default]

Subclonal states to consider. Default: [%default]

PICARD sequencing coverage. Default: [%default]

Initial Student's t precision; must contain 4 values (e.g. c(1500,1500,1500,1500)); if not provided then will automatically use based on variance of data. Default: [%default]

Hyperparameter (scale) for Gamma prior on Student's-t precision. Default: [%default]

Initial tumour ploidy; can be more than one value if additional ploidy initializations are desired. Default: [%default]

Total clonal CN states. Default: [%default]

Estimate subclonal prevalence. Default: [%default]

Estimate tumour ploidy. Default: [%default]

Exclude solutions with fraction of subclonal events greater than this value. Default: [%default]

Exclude solutions with subclonal genome fraction greater than this value. Default: [%default]

Minimum number of bins for largest segment threshold required to estimate tumor fraction; if below this threshold, then will be assigned zero tumor fraction.

Minimum proportion of bins altered required to estimate tumor fraction; if below this threshold, then will be assigned zero tumor fraction. Default: [%default]

Specify chromosomes to normalize GC/mappability biases. Default: [%default]

Specify chromosomes to estimate params. Default: [%default]

Specify chromosomes to analyze. Default: [%default]

If male, then normalize chrX by median. Default: [%default]

Threshold for fraction of reads in chrY to assign as male. Default: [%default]

If FALSE, then exclude HOMD state. Useful when using large bins (e.g. 1Mb). Default: [%default]