GenoFix

Using empirical and Bayesian probabilistic models of Mendelian inheritance to fix pedigree and genotypes

lib requirements

• python3
• pandas 1.3.4 pip3 install pandas
• matplotlib 3.4.3 pip3 install matplotlib
• seaborn 0.11.2 pip3 install seaborn
• pgmpy 0.1.16 pip3 install pgmpy
• networkx 2.6.2 pip3 install networkx
• numpy 1.21 pip3 install numpy
• tqdm 4.62.3 pip3 install tqdm
• cloudpickle 2.0.0 pip3 install cloudpickle
• pyarrow 8.0.0 pip3 install pyarrow
• mgzip pip3 install mgzip
• psutil pip3 install psutil
• sortedcontainers pip3 install sortedcontainers

or with conda...

conda create -n genofix python=3.10.0

source activate genofix

pip3 install pandas matplotlib seaborn pgmpy networkx numpy tqdm cloudpickle mgzip psutil sortedcontainers

main entry points

./genofix.py Correct a genotype matrix

./simulate/simulate.py Generate a gold standard genotype matrix (using random or by mating known founders and offspring to fill a pedigree), add known quantity of genotyping errors, and correct the genotype matrix (with statistics on precision and recall)

./utils/extract_founders.py Create a list of founders from a pedigree, which can be contrained with a genotype file when a more complete pedigree is part sequenced

./phase/evaluate.py Compare two phase prediction outputs in AlphaImpute2 format

./plotting/plot_rank_statistics.py Create histograms and heat maps for rank statistics created by simulate.py