Fix run.sh message

[mvelinder]

$ bash ~/bin/bAyesCMG/run.sh 
Make Sure you provide out all required parameters
Usage: VarBayes [OPTION]
 	Description of VarBayes
 		-h, --help Print help instructions
 		-v, --vcf_file Input VCF File Path [REQUIRED]
 		-p, --ped_file Input PED File Path [REQUIRED]
 		-r, --reference_file Reference (FASTA) File Path [REQUIRED]
 		-c, --get_clinvar Download latest ClinVar file [if no ClinVar file available in the data directory this arg will be ignored and ClinVar will be downloaded automatically reguardless]
 		-g, --gnomad GNOMAD File Path [REQUIRED]
 		-d, --vep_cache_dir VEP Cache Directory Path [REQUIRED]
 		-u, --vep_plugin_dir VEP Plugin Directory Path [REQUIRED]
 		-l, --vep_revel_file VEP REVEL File Path [REQUIRED]
 		-t, --gnomad_af_threshold gnomAD_AF threshold (default value = 0.01)
 		-j, --revel_af_threshold REVEL threshold [Ask Matt] (default value = 0.6)
 		-y, --prior_probability Prior probability [Optional, default 0.1]
 		-o, --odds_pathogenic The odds of pathogenicity for 'Very Strong' [Optional, default 350]
 		-e, --exponent The exponent that sets the strength of Supporting/Moderate/Strong compared to 'Very Strong' [Optional, default 0.1]
 		-f, --finished_vcf_path File name of the output vcf [REQUIRED]

• remove mention of VarBayes
• revel is not an af, make it revel_threshold
• remove all [Ask Matt]
• put all REQUIRED parameters together at the top, maybe even in their own section for easier visuals
• same as above for all OPTIONAL parameters
• change "Optional" to OPTIONAL to be consistent with REQUIRED
• fix typos like "reguardless"
• etc

[dillonl]

Done