idh1_config.yaml

input:
  id: idh1-test-sample
  mhc_alleles:
    - HLA-A*30:01
  # The input FASTQ files must live in the same directory as your config YAML file.
  # You should only need to modify the basename of the sample file paths, leaving the /inputs part
  # of the filename unchanged.
  normal:
    - fragment_id: L001
      # If your data is paired-end FASTQ files, you must specify the two files as r1 and r2 entries
      # instead of the singular r entry in this template. Also change the type to say paired-end.
      type: single-end
      r: /inputs/idh1_r132h_normal.fastq.gz
  tumor:
    - fragment_id: L001
      type: single-end
      r: /inputs/idh1_r132h_tumor.fastq.gz
  rna:
    - fragment_id: L001
      type: single-end
      r: /inputs/idh1_r132h_tumor.fastq.gz
# In most cases, you should not need to modify anything below this line.
workdir:
  /outputs
reference:
  genome: /reference-genome/b37decoy/b37decoy.fasta
  dbsnp: /reference-genome/b37decoy/dbsnp.vcf
  cosmic: /reference-genome/b37decoy/cosmic.vcf
  transcripts: /reference-genome/b37decoy/transcripts.gtf
  capture_kit_coverage_file: /reference-genome/b37decoy/S04380110_Covered_grch37_with_M.bed
parallel_indel_realigner: true
mhc_predictor: netmhcpan-iedb
variant_callers:
  - mutect
  - strelka