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parameters
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parameters
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[PARAMETER FILE for CellCoal] [text in brackets will be ignored]
[COALESCENT]
[number of replicates] n1
[number of ingroup cells] s10
[number of sites] l10
[effective population size] e10000
[demographics] [h2 1000 100 40000 200 30000 20000]
[exponential growth rate] g1e-5 [ln2=0.6931 max]
[birth rate] [K1]
[death rate] [L0.1]
[GENEALOGY MODIFIERS]
[root branch length ratio] k0.2
[outgroup branch length ratio] q1
[rate variation among branches] [i1]
[tree rate switches] N2 4 0.2
[MUTATION MODEL]
[alphabet binary:0 DNA:1] b1
[germline SNP rate] [c0.00001]
[somatic mutation rate] u1e-5
[CN_LOH rate] [H1e-5]
[deletion rate] [d1e-6]
[fixed number of mutations - ISM] j10
[trinucleotide genetic signature - ISM] [S1 1 1.0] [S2 11 0.3 22 0.7]
[default mutation model is ISM diploid]
[alternative mutation model ISMhap:0 Mk2:1 finiteDNA:2] m2
[proportion of alternative model sites] p0
[alternative/default model relative mutation rate] [w1]
[base frequencies] f0.3 0.2 0.2 0.3
[transition/transversion ratio] [t1.7]
[rate variation among sites] [a1.0]
[mutation matrix ACGT x ACGT] r0 1 1 1
1 0 1 1
1 1 0 1
1 1 1 0
[r0 1 2 3
1 0 4 5
2 4 0 1
3 5 1 0]
[r0.00 0.03 0.12 0.04
0.11 0.00 0.02 0.68
0.68 0.02 0.00 0.11
0.04 0.12 0.03 0.00]
[GENOTYPING PARAMETERS]
[genotyping error; no reads] [G0.1 0.01]
[scWGA PARAMETERS]
[fixed allelic dropout (ADO)] [D0.2]
[ADO per cell] [P0.1 0.01]
[ADO per site] [Q0.2 0.01]
[maternal allelic imbalance] [I0.5 0.01]
[amplification error] [A0.0003 0.0001 0]
[doublet rate per cell] [B0.02 0.01]
[NGS PARAMETERS]
[sequencing coverage; reads simulated] C30
[coverage overdispersion] [V5]
[haploid coverage] [R0.5]
[sequencing error] [E0.01]
[error matrix ACGT x ACGT] [X0 1 1 1
1 0 1 1
1 1 0 1
1 1 1 0]
[OUTPUT]
[print SNV genotypes] 1
[print SNV haplotypes] [2]
[print full genotypes] [3]
[print full haplotypes] [4]
[print root ancestors] [5]
[print trees] 6
[print times] [7]
[print CATG] [8]
[print PILEUP] [9]
[print true haplotypes] [Y]
[print consensus IUPAC sequences] x
[print replicates in individual folders] v
[results folder name] oresults
[user tree file] Tusertree.0001
[user genome file] [Uusergenome.fas]
[OTHER]
[use tumor nomenclature for cells] [W]
[noisy] y1
[seed] [#16106252] [if no seed is specified, the current time will be used as seed]
[noisy = 0: does not print anything
noisy = 1: + simulation summary,
noisy = 2: + replicate information,
noisy = 3: + calculation status and event information]