CONTAMINATION_WARN_FRACTION (0.2%), CONTAMINATION_REVIEW_FRACTION (1%), and the empirical p10 floor were all set from SRP434573 alone. The p10-floor estimator assumes a useful fraction of no-carrier sites and a particular allele-frequency spectrum, and even on clean data it reports a non-zero floor (~0.15% at 1% error, 2000x) from binomial sampling spread (shrinks as ~1/sqrt(depth)).
Measure the false-positive rate on genuinely uncontaminated high-depth samples and confirm the empirical floor behaves on panels with different marker allele frequencies. Validation work, not a code change, but it gates trusting any LoD floor built on the contamination estimate in deployment.
Evidence: [speculative]. Low priority (paper first). Was Step 32 in the retired overall plan.
CONTAMINATION_WARN_FRACTION(0.2%),CONTAMINATION_REVIEW_FRACTION(1%), and the empirical p10 floor were all set from SRP434573 alone. The p10-floor estimator assumes a useful fraction of no-carrier sites and a particular allele-frequency spectrum, and even on clean data it reports a non-zero floor (~0.15% at 1% error, 2000x) from binomial sampling spread (shrinks as ~1/sqrt(depth)).Measure the false-positive rate on genuinely uncontaminated high-depth samples and confirm the empirical floor behaves on panels with different marker allele frequencies. Validation work, not a code change, but it gates trusting any LoD floor built on the contamination estimate in deployment.
Evidence:
[speculative]. Low priority (paper first). Was Step 32 in the retired overall plan.