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# ffpe_artifacts.yaml — FFPE-damaged tumour sample
#
# Formalin-fixed paraffin-embedded (FFPE) tissue introduces characteristic
# sequencing artefacts that confound somatic variant calling:
#
# - C>T / G>A transitions from cytosine deamination (FFPE damage)
# - 8-oxoG lesions causing C>A / G>T transversions (oxidative damage)
# - Elevated PCR duplicate rate from degraded, short input DNA
#
# This configuration models a poorly preserved FFPE block with moderate
# deamination and oxidative damage. Suitable for benchmarking FFPE-aware
# variant callers and artefact-filtering pipelines.
#
# Run:
# varforge simulate --config examples/ffpe_artifacts.yaml
reference: ${reference} # set with --set reference=/path/to/hg38.fa
output:
directory: out/ffpe_artifacts
fastq: true
bam: true
truth_vcf: true
manifest: true
sample:
name: FFPE_TUMOUR
read_length: 150
coverage: 100.0
platform: illumina
# FFPE-derived DNA tends to be fragmented; shorter fragment distribution
# than fresh-frozen tissue.
fragment:
model: normal
mean: 180.0
sd: 60.0
quality:
mean_quality: 33 # FFPE quality slightly lower than fresh-frozen
tail_decay: 0.005
tumour:
purity: 0.40 # FFPE purity estimates are often lower due to necrosis
ploidy: 2
mutations:
random:
count: 500
vaf_min: 0.05
vaf_max: 0.40
snv_fraction: 0.80
indel_fraction: 0.15
mnv_fraction: 0.05
artifacts:
ffpe_damage_rate: 0.02 # 2% C>T deamination rate
oxog_rate: 0.01 # 1% 8-oxoG oxidative damage rate
duplicate_rate: 0.25 # elevated duplication from fragmented input
pcr_error_rate: 0.001 # slight PCR error elevation
seed: 9999
threads: 4