Template Script
/data2/bsi/RandD/Synthetic_Genomes/Synthetic_Tumor/genome_smasher_nar/actual_start.csh

Generating VCF RECORD
Scripts which generate the VCF records (sv.s and snv.s)
SNPS:  /data4/bsi/epibreast/m087494.couch/Development/Genome_Smasher/Scripts/SNP_mutator_v2.pl (apt)

SV.s wrapper (Includes insertions,deletions ,inversion ,CNV.s and Translocation.s)
/data4/bsi/epibreast/m087494.couch/Development/Genome_Smasher/SV_generator.sh


Sample VCF record file (Includes sv.s and snv.s)
/data2/bsi/RandD/Synthetic_Genomes/Synthetic_Tumor/genome_smasher_nar/All.variants.vcf



Actual Implementation [GENOME SIMULATOR]
/usr/bin/perl /data4/bsi/epibreast/m087494.couch//Development/Genome_Smasher/Scripts/perl_genome_simulator.pl 
 -refgenome_dir  /data2/bsi/reference/sequence/human/ncbi/37.1 -input_vcf_like /data2/bsi/RandD/Synthetic_Genomes/Synthetic_Tumor/genome_smasher_nar/All.variants.vcf
-ins_files_dir  /data2/bsi/RandD/Synthetic_Genomes/Synthetic_Tumor/genome_smasher_nar/INS_DIR/ 
-process_dir /data2/bsi/RandD/Synthetic_Genomes/Synthetic_Tumor/genome_smasher_nar/normal_genome
-fasta_length 60


FINAL VCF FILE CAN BE SEEN IN THE PROCESS DIRECTORY.

