Self-transition probability. Increase to decrease number of segments. Default: [%default]

Transition pseudo-counts. Exponent should be the same as the number of decimal places of --txnE. Default: [%default]

File format for output plots. Default: [%default]

ylim to use for chromosome plots. Default: [%default]

Script library path. Usually exclude this argument unless custom modifications have been made to the ichorCNA R package code and the user would like to source those R files. Default: [%default]

NaomicfDNA4_S3_R1.dedup.filt.bam.500Kb, n: 0.5, p: 2, log likelihood: 6124
NaomicfDNA4_S3_R1.dedup.filt.bam.500Kb, n: 0.5, p: 3, log likelihood: 5272
NaomicfDNA4_S3_R1.dedup.filt.bam.500Kb, n: 0.6, p: 2, log likelihood: 6805
NaomicfDNA4_S3_R1.dedup.filt.bam.500Kb, n: 0.6, p: 3, log likelihood: 5270
NaomicfDNA4_S3_R1.dedup.filt.bam.500Kb, n: 0.7, p: 2, log likelihood: 5769
NaomicfDNA4_S3_R1.dedup.filt.bam.500Kb, n: 0.7, p: 3, log likelihood: 5203
NaomicfDNA4_S3_R1.dedup.filt.bam.500Kb, n: 0.8, p: 2, log likelihood: 5795
NaomicfDNA4_S3_R1.dedup.filt.bam.500Kb, n: 0.8, p: 3, log likelihood: 5246
NaomicfDNA4_S3_R1.dedup.filt.bam.500Kb, n: 0.9, p: 2, log likelihood: 5794
NaomicfDNA4_S3_R1.dedup.filt.bam.500Kb, n: 0.9, p: 3, log likelihood: 5794