# —— Processing raw reads and mapping (Viola Nolte)
# QC_mapping.sh

# —— Processing BAM files and SNPs calling (Marlies Dolezal):
workflow.sh with config.txt

# —— Convert recombination map version 5 to 6
convert_recomb_map.R

# —— Convert BAM to sync files
convert_mapped_to_sync.sh

# —— Heterozygosity
heterozygosity.R

# —— Compute inversion frequencies
compute_inversion_freq.R

# —— Apply soft filters
apply_soft_filters.sh

# —— Apply hard filters and create parental SNPs set
create_SNPs_set.R

# —— Get AF over time
get_AF_over_time.R

# —— Set windows
set_windows.R

# ---- Perform neutral simulations chrom 2, 3 and X
perform_neutral_simulation.R: prepare hap files for simulations
mim_neutral_simulation.sh: MimicrEE2 command line 
read_neutral_simulation.R: read simulated sync 

# ---- Estimate Ne and s for each dataset
estimate_Ne_s.R

# ---- Perform the analysis
analysis_29_F20.R

# ---- Perform simulations with selection on X
perform_simulation_with_selection.R : prepare hap files for simulations
mim_simulation_with_selection.sh: MimicrEE2 command line 
read_simulation_with_selection.R: read simulated sync and compute goodness-of-fit criterion

# ---- Variables and functions
functions.R
global_variables.R
