projectTitle: "DROP: Detection of RNA Outliers Pipeline"
root: /mnt/NAS_DEPO_2/gtex_v8/output/drop1.3.3_star1_expcounts/output
htmlOutputPath: /mnt/NAS_DEPO_2/gtex_v8/output/drop1.3.3_star1_expcounts/html
indexWithFolderName: true

hpoFile: null
sampleAnnotation: /mnt/NAS_DEPO_2/gtex_v8/output/drop1.3.3_star1_expcounts/sample_annotation.tsv

geneAnnotation:
    v38: /mnt/NAS_DEPO_1/REF_GENOMES/HUMAN/hg38/GENCODE/GRCh38_gencode_v38/Genome/gencode.v38.primary_assembly.annotation.gtf
genomeAssembly: hg38
genome: 
    gencode_v38: /mnt/NAS_DEPO_1/REF_GENOMES/HUMAN/hg38/GENCODE/GRCh38_gencode_v38/Genome/GRCh38.primary_assembly.genome.fa

exportCounts:
    geneAnnotations:
        - v38       
    excludeGroups:
        - fraser

aberrantExpression:
    run: true
    groups:
        - outrider
    fpkmCutoff: 1
    implementation: autoencoder
    padjCutoff: 0.05
    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: 0.1
    maxTestedDimensionProportion: 6
    genesToTest: null
    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:
    qcGroups:
      - mae
    dnaRnaMatchCutoff: 0.85

rnaVariantCalling:
    run: false
    groups:
        - batch_0
    highQualityVCFs:
        - Data/Mills_and_1000G_gold_standard.indels.hg19.sites.chrPrefix.vcf.gz
        - Data/1000G_phase1.snps.high_confidence.hg19.sites.chrPrefix.vcf.gz
    dbSNP: Data/00-All.vcf.gz
    repeat_mask: Data/hg19_repeatMasker_sorted.chrPrefix.bed
    createSingleVCF: true
    addAF: true
    maxAF: 0.001
    maxVarFreqCohort: 0.05
    hcArgs: ""
    minAlt: 3
    yieldSize: 100000

tools:
    gatkCmd: gatk
    bcftoolsCmd: bcftools
    samtoolsCmd: samtools