config_analysis.yml

# Shared configurations
study:
    ibd: 'data/IBD_DeLange2017.sumstats.gz'
    cd: 'data/CD_DeLange2017.sumstats.gz'

features:
    - 'data/features/GTEx.txt'
    - 'data/features/mouse_brain2_diffexprs_tstat_clusters.txt'

gene_locations: 'assets/gene_locations__hg19.txt'
chromosomes: [ "21", "22" ]
loco: false # Leave one out method

# Stage 1: MAGMA
magma:
    description: "Settings for VCF QC module"

    annotate:
        description: "MAGMA annotation settings"
        run_process: true
        window_upstream_kb: 5
        window_downstream_kb: 5
    
    score_genes:
        description: "Settings to score genes"
        ld_reference: 'data/ld_reference/1000genomes_hg19_chr21_22'
        sumstat_n_col: 'N'
        sumstat_variant_id_col: 'SNP'
        sumstat_pvalue_col: 'PVAL'

# Stage 2: PoPs
pops:
    control_features: 'data/control_features.txt'
    permute_controls: true # true if control features should also be shuffled
    keep_hla_genes: false # Default is false

# Stage 3: Empirical PoPS analysis
empirical_pops:
    description: "Settings for running empirical PoPS"
    n_iterations: 4
    grouped: false
    use_absolute_value: false

    batch_iterations: false
    n_batch: 2