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

__OPTIONS_____________________________________________________________________

FASTA IN             	../input/random.fasta
SV SIZE TSV IN       	
VCF OUT              	random_var3.vcf
FASTA OUT            	random_var3.fasta
BREAKPOINT TSV OUT   	random_var3_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  	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/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.
