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input:
id: idh1-test-sample
# 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
# 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: false
variant_callers:
- mutect
- strelka