projectTitle: Detection of RNA Outlier Pipeline
htmlOutputPath: Output/html
indexWithFolderName: true
fileRegex: .*\.R

root: Output
sampleAnnotation: Data/sample_annotation.tsv
hpoFile: null
geneAnnotation:
    v29: Data/gencode_annotation_trunc.gtf
genomeAssembly: hg19
#genome: Data/chr21.fa #useful for future versions
scanBamParam: null
exportCounts:
  geneAnnotations:
    - v29
  excludeGroups:
    - mae

aberrantExpression:
    groups: 
      - outrider
    fpkmCutoff: 1
    implementation: autoencoder
    padjCutoff: 1
    zScoreCutoff: 0
    maxTestedDimensionProportion: 3
    dassie:
        tssWindow: 500
        pasWindow: 1000

aberrantSplicing:
    groups: 
      - fraser
    recount: true
    longRead: false
    keepNonStandardChrs: true
    filter: false
    minExpressionInOneSample: 20
    minDeltaPsi: 0.05
    implementation: PCA
    padjCutoff: 1
    zScoreCutoff: 0
    deltaPsiCutoff : 0.05
    maxTestedDimensionProportion: 6

mae:
    groups:
      - mae
    genome: Data/chr21.fa
    gatkIgnoreHeaderCheck: true
    padjCutoff: .05
    allelicRatioCutoff: 0.8
    addAF: false
    maxAF: .001
    maxVarFreqCohort: .04
    # VCF-BAM matching
    qcVcf: Data/qc_vcf_1000G.vcf.gz
    qcGroups:
      - mae

tools:
    gatkCmd: gatk
    bcftoolsCmd: bcftools
    samtoolsCmd: samtools

