parameters.yaml

### synth_generation_template.sh parameters ###

#path to working directory
working_directory: .
#folder for results
folder: results
#path to NEAT scripts
path_to_neat: /NEAT
#number of individual synth batches 
runs: 5
#seeds for each individual synth batch
rng: 213,214,215,217,218
#mutation rate parameter as taken from NEAT
mutation_rate: 0.1
#read length parameter as taken from NEAT
read_length: 100
#coverage parameter as taken from NEAT
coverage: 100
#fragment parameters as taken from NEAT
fragment_stats: 
 1: 300
 2: 30
#path to reference file
path_to_reference: /reference/TP53.fasta
#name of final merged bam file
output_bam_merged: Merged_auto


### variant_calling_template.sh parameters ###

#path to bam readcount scripts
path_to_bam_readcount: /home
#somatic variant caller name
caller: varscan
#path to varscan_scripts_path extra scripts
varscan_scripts_path: /Varscan2VCF
#genomic region of interest as taken from VarScan
vardict_region_of_interest: hg38_knownGene_ENST00000610292.4:0-19080