projectTitle: Detection of RNA Outlier test
root: /vcu_gpfs2/home/gaynora/DROP/udx_1037/Output
htmlOutputPath: /vcu_gpfs2/home/gaynora/DROP/udx_1037/Output/html
indexWithFolderName: true

hpoFile: null
sampleAnnotation: /vcu_gpfs2/home/gaynora/DROP/udx_1037/sample_annotation.tsv

geneAnnotation:
    v104: /vcu_gpfs2/home/gaynora/genomedirectory/collapsed_Homo_sapiens.GRCh38.104.gtf
genomeAssembly: hg38
genome:
    GRCh38: /vcu_gpfs2/home/gaynora/genomedirectory/Homo_sapiens.GRCh38.dna.primary_assembly.fa

#exportCounts:
    #geneAnnotations:
        #- v104
    #excludeGroups:
        #- mae
        #- outrider_external
        #- fraser_external

aberrantExpression:
    run: true
    groups:
        - outrider
    minlds: 1
    fpkmCutoff: 1
    implementation: autoencoder
    padjCutoff: 1.0
    zScoreCutoff: 0
    genesToTest: null
    maxTestedDimensionProportion: 3
    yieldSize: 2000000

aberrantSplicing:
    run: true
    groups:
        - fraser
    recount: false
    longRead: false
    keepNonStandardChrs: false
    filter: true
    minExpressionInOneSample: 20
    quantileMinExpression: 10
    minDeltaPsi: 0.05
    implementation: PCA
    padjCutoff: 1.0
    maxTestedDimensionProportion: 6
    genesToTest: null
    ### For FRASER2, use the follwing parameters instead of the 3 lines above:
    FRASER_version: "FRASER2"
    deltaPsiCutoff : 0.1
    quantileForFiltering: 0.75

mae:
    run: false
    groups:
        - group1
        - group2
        - group3
    gatkIgnoreHeaderCheck: true
    padjCutoff: 0.05
    allelicRatioCutoff: 0.8
    addAF: true
    maxAF: 0.001
    maxVarFreqCohort: 0.05
    # VCF-BAM matching
    qcVcf: Data/qc_vcf_1000G.vcf.gz
    qcGroups:
      - mae
    dnaRnaMatchCutoff: 0.85


rnaVariantCalling:
    run: true
    groups:
        - rnaVariantCalling
    highQualityVCFs:
        - /vcu_gpfs2/home/gaynora/DROP/variant_calling/resources_broad_hg38_v0_Homo_sapiens_assembly38.known_indels.vcf
        - /vcu_gpfs2/home/gaynora/DROP/variant_calling/resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf
    dbSNP: /vcu_gpfs2/home/gaynora/DROP/variant_calling/00-All.vcf.gz
    repeat_mask: /vcu_gpfs2/home/gaynora/DROP/variant_calling/hg38_repeatMasker_sorted.bed.gz
    createSingleVCF: true
    addAF: true
    maxAF: 0.001
    maxVarFreqCohort: 0.05
    hcArgs: ""
    minAlt: 3
    yieldSize: 100000

tools:
    gatkCmd: gatk
    bcftoolsCmd: bcftools
    samtoolsCmd: samtools