Configuration

Essential Setup (main.yaml)

Most users only need to modify these core settings:

Species and Populations (Human Example)

# Main configuration for species and data paths

testing_mode:  true  # Set to false for production analysis

# Species identification
species: "Human"

# Populations to analyze
populations:
  - YRI
  - CHS

# Data location and file naming
data:
  # Start with a small subset for testing 
  chromosomes:
     - 21
     - 22

  # Tell selscape how your VCF files are named
  vcf_files:
    base_path: "resources/data"
    file_prefix: ""
    file_suffix: ".vcf.gz"
    chr_name: "{ppl}.chr{i}"  # {ppl} = population, {i} = chromosome

  # Path to your sample metadata file
  metadata: "resources/data/1KG_metadata.txt"

# Reference genome
reference:
  species_code: "hg38"
  human_code: "hg38"

Method Parameters

Betascan (Balancing Selection) ```yaml

core_frequencies: - 0.15 # Most sensitive for detecting balancing selection

frequency_filters: min_af: 0.05 # Remove rare variants max_af: 0.95 # Remove nearly fixed variants

folding: use_folded: true # Use if you don't have ancestral states **Selscan (Positive Selection)**yaml data_type: unphased: true # Set to false if you have phased data

statistics: within_population: [ihs, nsl] cross_population: [xpehh, xpnsl]

frequency_filters: maf_thresholds: [0.05] # Minor allele frequency cutoff ```

Advanced Configuration

main.yaml Parameters

Parameter	Type	Description	Default
testing_mode	boolean	Use example data for testing	false
species	string	Species identifier for outputs	"Human"
populations	list	Population code to analyze	["YRI", "CHS"]
data.chromosomes	list	Chromosomes to include	[21, 22]
data.vcf_files.base_path	string	VCF file directory	"resources/data"
data.vcf_files.chr_name	string	Chromosome naming pattern	"{ppl}.chr{i}"
reference.species_code	string	Reference genome build	"hg38"
data.metadata	string	Sample metadata file path	"resources/data/1KG_metadata.txt"
data.vcf_files.file_prefix	string	VCF filename prefix	""
data.vcf_files.file_suffix	string	VCF filename suffix	".vcf.gz"
data_sources	dict	Data source configurations	see config
reference.annotation_reference	string	Reference genome for annotation databases	"hg38"

betascan.yaml Parameters | Parameter |Type |Description | Default | |----------------|-------------------------------|-----------------------------|-----------------------------| |core_frequencies|list |Core allele frequencies for B1 | [0.15]| |frequency_filters.min_af |float |Minimum allele frequency |0.05 | |frequency_filters.max_af |float|Maximum allele frequency|0.95 | |folding.use_folded |boolean|Use folded SFS|true | |thresholds.top_percent |float|Top % for candidates|0.0005 | |quality_control.hwe_pvalue|float|Hardy-Weinberg p-value threshold|0.001| |quality_control.mask_repeats|boolean|Exclude repetitive regions|true|

selscan.yaml Parameters | Parameter |Type |Description | Default | |----------------|-------------------------------|-----------------------------|-----------------------------| |data_type.unphased|boolean |Handle unphased data | true| |statistics.within_population |list | Within-pop statistics |[ihs, nsl] | |statistics.cross_population |list|Cross-pop statistics|[xpehh, xpnsl] | |frequency_filters.maf_thresholds |list|MAF cutoffs|[0.05] |

dadi-cli.yaml Parameters | Parameter |Type |Description | Default | |----------------|-------------------------------|-----------------------------|-----------------------------| |flags.ratio|float |Transition/transversion ratio | 2.31| |flags.optimizations |integer|Number of optimization runs | 50| |grid_size.inference |string|Grid size for inference| "300 400 500"| |gamma_pts |integer|Gamma integration points| 2000| |grid_size.cache|string|Grid size for caching|"800 1000 1200"| |flags.bootstrap_replicates|integer|Bootstrap replicates|100| |flags.chunk_size|integer|Chunk size for bootstrap|1000000|

annovar.yaml Parameters |Parameter|Type|Description|Default| |----------------|-------------------------------|-----------------------------|-----------------------------| |species.{species}.genome_build|string|Reference genome build|"hg38"| |settings.threads|integer|Annotation threads|8|

Please check Snakemake Configuration documentation for additional information.