Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
How to import GATK reports into Python/pandas DataFrames
Answering my own question. I searched around and could not find a Python equivalent to the gsalib R library, which enables R analysis of GATK reports produced by VariantEval and other tools. So I created a port of the R gsalib to a Python module. The
GatkReport object will read a report file (supports v0 and v1), and load each table into a pandas DataFrame.
pip install gsalib.
from gsalib import GatkReport report = GatkReport('/path/to/gsalib/test/test_v1.0_gatkreport.table') table = report.tables['ExampleTable']