npybio-ngsdata

Notebook ipython to parse and handle NGS Data for variants.

## Input data

Upload of [CSV](missing reference), [TSV](missing reference), or [VCF](missing reference)

formatted files, already annotated.

A suggested software for annotation is [ANNOVAR](missing reference).

All files should be inside an 'input/' directory available at the same level of the running notebook.

# Clone repo
cd /tmp
git clone https://github.com/pdonorio/npybio-ngsdata.git nbs

# Launch notebook server
docker run -d --name ipy -p 80:8000 -v /tmp/nbs:/home/pydatanalysis/nbs pdonorio/ipynb_data_slides

# visit http://localhost
# username: pydatanalysis, password: workshop

## How it works

This notebooks examples help to parse, filter, plot and intersect annotated variants via python commands.

Debugging

Download the python code and the package from notebook and execute it via shell. There will prompt logger prints.