ucsc-cgl-synthetic-genomes

Anders Poirel

Dependencies

• Popper
• Docker

Container enginer configuration

If using Docker, and on a host OS where the files you wish to use require permission to access, edit config.yml and change user to have the appropiate uid. Use the --conf config.yml with every call to Popper.

Note: depending on the machine, additional configuration may be required to use the GPU.

Running all steps in the workflow

popper run -f wf.yml 

Generating synthetic samples

GAN

TODO

Naive (Null) model

With Popper

Change the steps in wf.yml to reflect the input and output files you wish to use

popper run -f wf.yml naive_fit
popper run -f wf.yml naive_generation

Without Popper

Run

docker run -it --mount ./ ./containers/allel/

In the container,

python src/frequency_model/sample_frequencies.py \
    data/raw/brca2.vcf \
    output/models/brca2_freqs.json &&

python src/frequency_generation/generate_naive_samples.py \
    generate_naive_samples.py \
    -n 10000 \
    output/models/brca2_freqs.json \
    output/samples/naive_samples.vcf 

Omit the first command if sample_freqs.json already exists

References

My term papers with explanations of relevant theoretical aspects are here.