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

myourshawmyourshaw University of ColoradoMember ✭✭
edited March 2018 in Ask the GATK team

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.

Install with: pip install gsalib.

Example usage:

from gsalib import GatkReport

report = GatkReport('/path/to/gsalib/test/test_v1.0_gatkreport.table')
table = report.tables['ExampleTable']
Post edited by myourshaw on


Sign In or Register to comment.