projectTitle: 'DROP: Detection of RNA Outliers Pipeline'
root: /home/gbergant/DROP/outputs
htmlOutputPath: /home/gbergant/DROP/outputs
indexWithFolderName: true
hpoFile: /home/gbergant/DROP/RNAseq_databases/hpo_genes.tsv.gz
sampleAnnotation: /home/gbergant/DROP/drop_wd/sample_annotation.tsv
random_seed: 'true'
geneAnnotation:
  v43: /home/gbergant/DROP/RNAseq_databases/gencode.v43lift37.basic.annotation.gtf
genomeAssembly: hg19
genome: /home/gbergant/DROP/RNAseq_databases/hg19_fa/hg19.fa
exportCounts:
  geneAnnotations:
  - v43
aberrantExpression:
  run: true
  groups:
  - AE
  minIds: 1
  fpkmCutoff: 1
  implementation: autoencoder
  padjCutoff: 1
  zScoreCutoff: 0
  maxTestedDimensionProportion: 3
  genesToTest: /home/gbergant/DROP/RNAseq_databases/myopathies3panels.yaml
aberrantSplicing:
  run: true
  groups:
  - AS
  minIds: 1
  recount: false
  longRead: false
  keepNonStandardChrs: false
  filter: true
  minExpressionInOneSample: 20
  quantileMinExpression: 10
  quantileForFiltering: 0.95
  minDeltaPsi: 0.05
  implementation: PCA
  FRASER_version: FRASER
  deltaPsiCutoff: 0.3
  padjCutoff: 1
  maxTestedDimensionProportion: 6
  genesToTest: /home/gbergant/DROP/RNAseq_databases/myopathies3panels.yaml
mae:
  run: true
  groups:
  - MAE
  gatkIgnoreHeaderCheck: true
  padjCutoff: 0.05
  allelicRatioCutoff: 0.8
  addAF: 'true'
  maxAF: 0.001
  maxVarFreqCohort: 0.3
  qcVcf: /home/gbergant/DROP/RNAseq_databases/hg19_common_sites/qc_vcf_1000G_hg19.vcf.gz
  qcGroups:
  - MAE
  dnaRnaMatchCutoff: 0.85
rnaVariantCalling:
  run: false
tools:
  gatkCmd: gatk
  bcftoolsCmd: bcftools
  samtoolsCmd: samtools