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dapogon committed Jun 11, 2019
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87 changes: 87 additions & 0 deletions examples/parameters.GTR.reads
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[PARAMETER FILE for CellCoal] [text in brackets will be ignored]

[COALESCENT]
[number of replicates] n10
[number of cells] s10
[number of sites] l1000
[effective population size] e10000
[demographics] [h2 1000 100 40000 200 30000 20000]
[exponential growth rate] g1e-4 [ln2=0.6931 max]

[GENEALOGY MODIFIERS]
[root branch length ratio] k0.1
[outgroup branch length ratio] q0.2
[rate variation among branches] i1

[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] [j100]
[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] p1
[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]

[NGS PARAMETERS]
[genotyping error; no reads] [G0.1]
[sequencing coverage; reads simulated] C60
[coverage overdispersion] V5
[mat/pat allelic imbalance] [I0.5]
[ADO:allelic dropout] D0.2
[ADO variation among sites] [P1.0]
[ADO variation among cells] [Q1.0]
[haploid coverage] [R0.5]
[amplification error] A0.5 0.01 0
[sequencing error] E0.01
[doublet rate per cell] [B0.0]
[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 true haplotypes] [9]
[print replicates in individual folders] v
[print consensus IUPAC haplotypes] [x]
[results folder name] oresults_GTR_reads
[user tree file] [Tusertree.0001]
[user genome file] [Uusergenome.fas]

[OTHER]
[use tumor nomenclature for cells] [W]
[noisy] y1
[seed] [#1542634305] [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]

87 changes: 87 additions & 0 deletions examples/parameters.ISM.binary
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[PARAMETER FILE for CellCoal] [text in brackets will be ignored]

[COALESCENT]
[number of replicates] n10
[number of cells] s1000
[number of sites] l200
[effective population size] e10000
[demographics] [h2 1000 100 40000 200 30000 20000]
[exponential growth rate] g1e-5 [ln2=0.6931 max]

[GENEALOGY MODIFIERS]
[root branch length ratio] k0.1
[outgroup branch length ratio] q0.2
[rate variation among branches] [i1]

[MUTATION MODEL]
[alphabet binary:0 DNA:1] b0
[germline SNP rate] [c0.00001]
[somatic mutation rate] u1e-5
[CN_LOH rate] [H1e-5]
[deletion rate] [d1e-6]
[fixed number of mutations - ISM] j99
[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] [m0]
[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]

[NGS PARAMETERS]
[genotyping error; no reads] G0.0
[sequencing coverage; reads simulated] [C100]
[coverage overdispersion] [V5]
[mat/pat allelic imbalance] [I0.5]
[ADO:allelic dropout] D0
[ADO variation among sites] [P1.0]
[ADO variation among cells] [Q1.0]
[haploid coverage] [R0.5]
[amplification error] [A0.5 0.01 0]
[sequencing error] E0.01
[doublet rate per cell] [B0.0]
[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 true haplotypes] [9]
[print replicates in individual folders] v
[print consensus IUPAC haplotypes] [x]
[results folder name] oresults_ISM_binary
[user tree file] [Tusertree.0001]
[user genome file] [Uusergenome.fas]

[OTHER]
[use tumor nomenclature for cells] [W]
[noisy] y1
[seed] [#1542634305] [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]

87 changes: 87 additions & 0 deletions examples/parameters.ISM.usergenome
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[PARAMETER FILE for CellCoal] [text in brackets will be ignored]

[COALESCENT]
[number of replicates] n10
[number of cells] s40
[number of sites] l1000
[effective population size] e10000
[demographics] [h2 1000 100 40000 200 30000 20000]
[exponential growth rate] g1e-5 [ln2=0.6931 max]

[GENEALOGY MODIFIERS]
[root branch length ratio] k0.1
[outgroup branch length ratio] q0.2
[rate variation among branches] [i1]

[MUTATION MODEL]
[alphabet binary:0 DNA:1] b1
[germline SNP rate] [c0.00001]
[somatic mutation rate] u1e-6
[CN_LOH rate] [H1e-5]
[deletion rate] d1e-7
[fixed number of mutations - ISM] [j100]
[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] [m0]
[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]

[NGS PARAMETERS]
[genotyping error; no reads] G0.0
[sequencing coverage; reads simulated] [C100]
[coverage overdispersion] [V5]
[mat/pat allelic imbalance] [I0.5]
[ADO:allelic dropout] D0
[ADO variation among sites] [P1.0]
[ADO variation among cells] [Q1.0]
[haploid coverage] [R0.5]
[amplification error] [A0.5 0.01 0]
[sequencing error] [E0.01]
[doublet rate per cell] [B0.0]
[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 true haplotypes] [9]
[print replicates in individual folders] v
[print consensus IUPAC haplotypes] [x]
[results folder name] oresults_ISM_usergenome
[user tree file] [Tusertree.0001]
[user genome file] Uusergenome.fas

[OTHER]
[use tumor nomenclature for cells] [W]
[noisy] y1
[seed] [#1542634305] [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]

87 changes: 87 additions & 0 deletions examples/parameters.JC.usertree
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[PARAMETER FILE for CellCoal] [text in brackets will be ignored]

[COALESCENT]
[number of replicates] n100
[number of cells] s8
[number of sites] l1000
[effective population size] e10000
[demographics] [h2 1000 100 40000 200 30000 20000]
[exponential growth rate] g1e-4 [ln2=0.6931 max]

[GENEALOGY MODIFIERS]
[root branch length ratio] k0.1
[outgroup branch length ratio] q0.2
[rate variation among branches] [i1]

[MUTATION MODEL]
[alphabet binary:0 DNA:1] b0
[germline SNP rate] [c0.00001]
[somatic mutation rate] u1e-6
[CN_LOH rate] H1e-7
[deletion rate] [d1e-7]
[fixed number of mutations - ISM] [j100]
[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] [m0]
[proportion of alternative model sites] p1
[alternative/default model relative mutation rate] [w1]
[base frequencies] f0.25 0.25 0.25 0.25
[transition/transversion ratio] t0.5
[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]

[NGS PARAMETERS]
[genotyping error; no reads] G0.0
[sequencing coverage; reads simulated] [C100]
[coverage overdispersion] [V5]
[mat/pat allelic imbalance] [I0.5]
[ADO:allelic dropout] D0
[ADO variation among sites] [P1.0]
[ADO variation among cells] [Q1.0]
[haploid coverage] [R0.5]
[amplification error] [A0.5 0.01 0]
[sequencing error] [E0.01]
[doublet rate per cell] [B0.0]
[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 true haplotypes] [9]
[print replicates in individual folders] v
[print consensus IUPAC haplotypes] [x]
[results folder name] oresults_JC_usertree
[user tree file] Tusertree.0001
[user genome file] [Uusergenome.fas]

[OTHER]
[use tumor nomenclature for cells] [W]
[noisy] y2
[seed] [#1542634305] [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]

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