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.1Mb, n: 0.5, p: 2, log likelihood: 3350
NaomicfDNA2_S2_R1.dedup.filt.bam.1Mb, n: 0.5, p: 3, log likelihood: 2335
NaomicfDNA2_S2_R1.dedup.filt.bam.1Mb, n: 0.6, p: 2, log likelihood: 2805
NaomicfDNA2_S2_R1.dedup.filt.bam.1Mb, n: 0.6, p: 3, log likelihood: 2605
NaomicfDNA2_S2_R1.dedup.filt.bam.1Mb, n: 0.7, p: 2, log likelihood: 2898
NaomicfDNA2_S2_R1.dedup.filt.bam.1Mb, n: 0.7, p: 3, log likelihood: 2595
NaomicfDNA2_S2_R1.dedup.filt.bam.1Mb, n: 0.8, p: 2, log likelihood: 2898
NaomicfDNA2_S2_R1.dedup.filt.bam.1Mb, n: 0.8, p: 3, log likelihood: 2595
NaomicfDNA2_S2_R1.dedup.filt.bam.1Mb, n: 0.9, p: 2, log likelihood: 2898
NaomicfDNA2_S2_R1.dedup.filt.bam.1Mb, n: 0.9, p: 3, log likelihood: 2898