MetaDenovo_UserInputs.json

{
  "##_COMMENT1": "Trio INPUT BAMs",
  "MetaDenovo_workflow.mother_bam": "s3://<your S3 location for mother.bam>",
  "MetaDenovo_workflow.mother_bam_bai": "s3://<your S3 location for mother.bam.bai>",
  "MetaDenovo_workflow.father_bam": "s3://<your S3 location for father.bam>",
  "MetaDenovo_workflow.father_bam_bai": "s3://<your S3 location for father.bam.bai>",
  "MetaDenovo_workflow.child_bam": "s3://<your S3 location for child.bam>",
  "MetaDenovo_workflow.child_bam_bai": "s3://<your S3 location for child.bam.bai>",
  "##_COMMENT2": "chromosome IDs",
  "MetaDenovo_workflow.chromosome_ids": [
    1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
  ],
  "##_COMMENT3": "Reference files",
  "MetaDenovo_workflow.reference": "s3://<your S3 location for fa/fna file>",
  "MetaDenovo_workflow.reference_fai": "s3://<your S3 location for fa/fna fai file>",
  "MetaDenovo_workflow.reference_dict": "s3://<your S3 location for dict file>",
  "##_COMMENT4": "PEDIGREE File",
  "MetaDenovo_workflow.ped_file": "s3://<your S3 location for family.ped>",
  "##_COMMENT5": "GATK Output Trio VCF File",
  "MetaDenovo_workflow.gatk_vcf": "s3://<your S3 location for gatk.vcf>",
  "##_COMMENT6": "code extend files",
  "MetaDenovo_workflow.python_file": "s3://<your S3 location>/code_extend/DenovoGear_numeric_genotype.py",
  "MetaDenovo_workflow.selectDNMGenotype_program": "s3://<your S3 location>/code_extend/TrioDenovo_select_DNM_genotype.py"
}