projectTitle: Detection of RNA Outlier Pipeline htmlOutputPath: Output/html indexWithFolderName: true root: Output sampleAnnotation: Data/sample_annotation.tsv hpoFile: null geneAnnotation: v29: Data/gencode_annotation_trunc.gtf genomeAssembly: hg19 genome: Data/chr21.fa 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 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