mutect2.inputs.json

{
  "Mutect2.gatk_docker": "broadinstitute/gatk:4.1.4.1",
  "ref_local_path": "/mnt/nfs/ref/",

  "Mutect2.intervals": "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list",
  "Mutect2.scatter_count": 50,
  "Mutect2.m2_extra_args": "--downsampling-stride 20 --max-reads-per-alignment-start 6 --max-suspicious-reads-per-alignment-start 6",
  "Mutect2.filter_funcotations": "True",
  "Mutect2.funco_transcript_selection_list": "transcriptList.exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt",

  "Mutect2.ref_fasta": "Homo_sapiens_assembly19.fasta",
  "Mutect2.ref_dict": "Homo_sapiens_assembly19.dict",
  "Mutect2.ref_fai": "Homo_sapiens_assembly19.fasta.fai",

  "Mutect2.pon": "Mutect2-exome-panel.vcf",
  "Mutect2.pon_idx": "Mutect2-exome-panel.vcf.idx",
  "Mutect2.gnomad": "af-only-gnomad.raw.sites.vcf",
  "Mutect2.gnomad_idx": "af-only-gnomad.raw.sites.vcf.idx",
  "Mutect2.variants_for_contamination": "small_exac_common_3.vcf",
  "Mutect2.variants_for_contamination_idx": "small_exac_common_3.vcf.idx",
  "Mutect2.realignment_index_bundle": "Homo_sapiens_assembly38.index_bundle",
  
  "onco_folder": "funco_slim"
}