UserInputs_demo.json

{
  "##_COMMENT1": "Trio INPUT BAMs",
  "MetaDenovo_workflow.mother_bam": "s3://vccri-giannoulatou-lab-denovo-mutations/MetaDenovo/demo_data/NA12892_demo.bam",
  "MetaDenovo_workflow.mother_bam_bai": "s3://vccri-giannoulatou-lab-denovo-mutations/MetaDenovo/demo_data/NA12892_demo.bam.bai",
  "MetaDenovo_workflow.father_bam": "s3://vccri-giannoulatou-lab-denovo-mutations/MetaDenovo/demo_data/NA12891_demo.bam",
  "MetaDenovo_workflow.father_bam_bai": "s3://vccri-giannoulatou-lab-denovo-mutations/MetaDenovo/demo_data/NA12891_demo.bam.bai",
  "MetaDenovo_workflow.child_bam": "s3://vccri-giannoulatou-lab-denovo-mutations/MetaDenovo/demo_data/NA12878_demo.bam",
  "MetaDenovo_workflow.child_bam_bai": "s3://vccri-giannoulatou-lab-denovo-mutations/MetaDenovo/demo_data/NA12878_demo.bam.bai",
  "##_COMMENT2": "chromosome IDs",
  "MetaDenovo_workflow.chromosome_ids": [
    22
  ],
  "##_COMMENT3": "Reference files",
  "MetaDenovo_workflow.reference": "s3://vccri-giannoulatou-lab-denovo-mutations/MetaDenovo/demo_data/chr22.fa",
  "MetaDenovo_workflow.reference_fai": "s3://vccri-giannoulatou-lab-denovo-mutations/MetaDenovo/demo_data/chr22.fa.fai",
  "MetaDenovo_workflow.reference_dict": "s3://vccri-giannoulatou-lab-denovo-mutations/MetaDenovo/demo_data/chr22.dict",
  "##_COMMENT4": "PEDIGREE File",
  "MetaDenovo_workflow.ped_file": "s3://vccri-giannoulatou-lab-denovo-mutations/MetaDenovo/demo_data/CEPH_trio_30x_noheader.ped",
  "##_COMMENT5": "GATK Output Trio VCF File",
  "MetaDenovo_workflow.gatk_vcf": "s3://vccri-giannoulatou-lab-denovo-mutations/MetaDenovo/demo_data/input_gatk_demo.vcf",
  "##_COMMENT6": "code extend files",
  "MetaDenovo_workflow.python_file": "s3://vccri-gwfcore-mictro/CHD_Jan_2023/Metadenovo_demo_test2/code_extend/DenovoGear_numeric_genotype.py",
  "MetaDenovo_workflow.selectDNMGenotype_program": "s3://vccri-gwfcore-mictro/CHD_Jan_2023/Metadenovo_demo_test2/code_extend/TrioDenovo_select_DNM_genotype.py"
}