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Configuration

config.yaml

Unified pipeline configuration. All paths are relative to the repository root.

Required Fields

Field Type Description
paths.samples string Path to samples TSV
paths.vcf_folder string Directory with input VCF files
paths.output_folder string Root output directory
snpeff.database string snpEff database name (e.g., GRCh37.p13)
snpsift.dbnsfp_db string Path to dbNSFP database file (v4.x or v5.x)
snpsift.dbnsfp_fields string Comma-separated dbNSFP fields (auto-selected for v4/v5 by config generator)
scatter.mode string "none", "chromosome", or "interval"

Required for Scatter Modes (scatter.mode: "chromosome" or "interval")

Field Description
ref.genome Path to reference genome FASTA
ref.dict Path to reference sequence dictionary
scatter.count Number of scatter intervals (default: 100, interval mode only)
scatter.canonical_contigs List of canonical contigs to include (used by both chromosome and interval modes)

Optional Fields

Field Default Description
paths.log_subdir "logs" Log subdirectory name
paths.annotation_subdir "annotation" Annotation subdirectory name
snpeff.extra_flags "" Additional snpEff flags
extra_annotations [] List of extra VCF annotation steps

dbNSFP Field Lists

The config generator auto-detects the dbNSFP major version from the database filename and selects the appropriate field list:

dbNSFP version Key differences
v4.x LRT, FATHMM, gnomAD exomes/genomes (separate), MutationTaster_converted_rankscore
v5.x LRT retired, FATHMM replaced by fathmm-XF, gnomAD merged into gnomAD4.1 joint, MutationTaster_rankscore

If you change the dbNSFP database version after generating config, regenerate with scripts/generate_config.py or manually update snpsift.dbnsfp_fields.

Extra Annotations

Each entry in extra_annotations applies one SnpSift annotate step:

extra_annotations:
  - vcf_file: "/path/to/annotation.vcf.gz"
    info_field: "AF"
    annotation_prefix: "MYDB_"

samples.tsv

Tab-separated sample metadata. Required columns:

Column Description
sample Unique sample identifier
vcf_basename VCF file basename (without .vcf.gz extension)