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]

NaomicfDNA2_S2_R1.dedup.filt.bam.500Kb, n: 0.5, p: 2, log likelihood: 5486
NaomicfDNA2_S2_R1.dedup.filt.bam.500Kb, n: 0.5, p: 3, log likelihood: 5171
NaomicfDNA2_S2_R1.dedup.filt.bam.500Kb, n: 0.6, p: 2, log likelihood: 5469
NaomicfDNA2_S2_R1.dedup.filt.bam.500Kb, n: 0.6, p: 3, log likelihood: 5190
NaomicfDNA2_S2_R1.dedup.filt.bam.500Kb, n: 0.7, p: 2, log likelihood: 5665
NaomicfDNA2_S2_R1.dedup.filt.bam.500Kb, n: 0.7, p: 3, log likelihood: 5233
NaomicfDNA2_S2_R1.dedup.filt.bam.500Kb, n: 0.8, p: 2, log likelihood: 5665
NaomicfDNA2_S2_R1.dedup.filt.bam.500Kb, n: 0.8, p: 3, log likelihood: 5233
NaomicfDNA2_S2_R1.dedup.filt.bam.500Kb, n: 0.9, p: 2, log likelihood: 5664
NaomicfDNA2_S2_R1.dedup.filt.bam.500Kb, n: 0.9, p: 3, log likelihood: 5664