config.yaml

## path to output folder, please end with a backslash or you'll have problems
outputdir:  /data/browna6/evolution/facets/sclc/
# parameters given by the authors for the snp pileup, except -d, which I had increased from the default of 4000 since
#we had quite high depth with very large copy number increases
#-g compress output file with GFZF
#q, --min-map-quality=QUALITY   Sets the minimum threshold for mapping quality. Default is 0.
#-Q
snppileup_parms: "-g -q15 -Q20 -P100 -r25,0 -d10000"
#this is a vcf of the common human snps, make sure it's the right build
snpVCF: /path/to/common_all.vcf.gz
snppilepath: ./snp-pileup
#the is the file path to the run_facets.R script
path_to_run_r: /path/to/run_facets.R
#the minimum number of hetrozygous snps used to call the minor copy number by FACETS, unless you have a compelling reason
#to change this, e.g. you need the minor copy numbers of a given gene, and there aren't many hetrozygous snps at that location
#then it's best to keep it at the default suggested by the authors
minimum_nhet: 15
#change this desired output folder
outputdirPhyloInput:  /data/output/
#change this to point to the new sample set. 
sampleCSVpath: /data/samples.csv