martinghunt
commented
4 years ago - Fixes bug where simulations to determine GCP distribution were always using het genotyping model, even if the run is only using hom model.
- bug fix meant that GCP shifted a little. Consequently, change default MIN_GCP filter from 5% to 2.5%.
- Change default MIN_DP filter from 0 to 2.
- Use negative binomial distribution for everything, instead of poisson. Fall back on poisson if coverage is too low.