COVID-Pooling

Install

conda env create -n covid-pooling python=3.7
conda activate covid-pooling
conda config --add channels r
conda config --add channels bioconda
conda install pysam numpy matplotlib scipy pathos

Usage

1. Estimate posterior probabilities for the individual reads

python estimate_posteriors_reads_s.py.py variants.csv reads.bam -o posteriors.csv -t 10 --subst_rate 0.05 

Output: posteriors.csv

2. Count the reads profile with filtering uncertain reads

python count_observed_counts_filtering_uncertain.py ref.fa reads.bam posteriors.csv -c 0.75 -o observed.csv

Output: observed.csv

3. Estimate the variant proportions

python fastend_cpp_s.py observed.csv variants.csv --no-jacobian -t 4 -n 10 -o calculations.yaml

Output: calculations.yaml

4. Extract the final result

python extract_weights.py calculations.yaml result.yaml

Output: result.yaml