MASON VARIATOR
==============

__OPTIONS_____________________________________________________________________

FASTA IN             	../input/adeno_virus.fa
SV SIZE TSV IN       	
VCF OUT              	random_var9.vcf
FASTA OUT            	random_var9.fasta
BREAKPOINT TSV OUT   	
METHYLATION IN FILE  	

GENERATE VAR IDS     	YES

NUM HAPLOTYPES       	1
HAPLOTYPE SEP        	"/"

SNP RATE             	0.0001
SMALL INDEL RATE     	1e-06

MIN SMALL INDEL SIZE 	1
MAX SMALL INDEL SIZE 	6

SV INDEL RATE        	0.01
SV INVERSION RATE    	0.01
SV TRANSLOCATION RATE	1e-07
SV DUPLICATION RATE  	0.01

MIN SV SIZE          	20
MAX SV SIZE          	300

SIM. METHYL. LEVELS  	0
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 ../input/adeno_virus.fa ... OK (1 seqs)

__SIMULATION__________________________________________________________________


Simulation...
  gi|56160436|ref|AC_000005.1|
  snps:                2
  small indels:        0
  structural variants: 177
OK.


DONE.
