1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
|
MASON VARIATOR
==============
__OPTIONS_____________________________________________________________________
FASTA IN random.fasta
SV SIZE TSV IN
VCF OUT random_var1.vcf
FASTA OUT random_var1.fasta
BREAKPOINT TSV OUT random_var1_bp.txt
METHYLATION IN FILE
GENERATE VAR IDS YES
NUM HAPLOTYPES 2
HAPLOTYPE SEP "/"
SNP RATE 0.001
SMALL INDEL RATE 0.001
MIN SMALL INDEL SIZE 1
MAX SMALL INDEL SIZE 6
SV INDEL RATE 0.001
SV INVERSION RATE 0.001
SV TRANSLOCATION RATE 0.001
SV DUPLICATION RATE 0.001
MIN SV SIZE 50
MAX SV SIZE 100
SIM. METHYL. LEVELS 1
METHYLATION LEVELS
CG MU 0.6
CG SIGMA 0.03
CHG MU 0.08
CHG SIGMA 0.008
CHH MU 0.05
CHH SIGMA 0.005
__PREPARATION_________________________________________________________________
Loading Reference Index random.fasta ... OK (2 seqs)
__SIMULATION__________________________________________________________________
Simulation...
1
snps: 18
small indels: 10
structural variants: 35
2
snps: 0
small indels: 1
structural variants: 2
OK.
DONE.
|
