config.yaml

################################################################################
## Carrot demography - Configuration file
## This is a handy way to set file paths and variables (e.g. mutation rate) so
## that they are easily adjusted
################################################################################

# file path for population and sample ids
# Two column tab-delimited file
# Column names: Population, Sample_ID
samp_ids: data/sample_ids_admix10.txt

# list of distinguished individuals to use for composite likelihood
distinguished_inds: data/distinguished_individuals_admix10.txt

# VCF file & index
# can create index by using tabix -p vcf yourfile.vcf.gz
# vcf: data/kevinG.d3.recode.vcf.gz
# vcf_index: data/kevinG.d3.recode.vcf.gz.tbi
vcf: data/kevinG.d3.recode.missing10.vcf.gz
vcf_index: data/kevinG.d3.recode.missing10.vcf.gz.tbi

# mask file to exclude poorly mapped regions (BED format)
# should be a text file with a column for CHR, start, & stop positions
# this result is from RepeatMasker but could also use SNPable
mask: data/masked_regions.bed.gz

# estimate of per bp per generation mutation rate for SMC++
# taken from lettuce (Asterid) - Zhang et al. doi:10.1038/s41467-017-02445-9
mu: 4e-8

# number of years per generation
gen: 2