gsalib makes it easy for Python users to analyze metrics reports created by the Broad Institute's Genome Analysis Toolkit (GATK). The Broad provides an R library called gsalib that allows you to load GATKReport files into R for further analysis (https://gatkforums.broadinstitute.org/gatk/discussion/1244/what-is-the-gatkreport-file-format). Python gsalib is an adaptation of the R libray that allows you to load GATKReport files into Python/pandas DataFrames.
Neither the R nor Python versions of gsalib support the samtools.metrics reports created by Picard Tools. To analyze Picard reports with Python, consider using the picard.parse function in the Crimson module.
- Enables analysis of GATK reports with powerful pandas DataFrames and plotting
- Reads GATKReport versions 0.x and 1.x
- Compatible with Python >=2.7 and >=3.4
Install gsalib by running
pip install gsalib
Read a report and get a table's DataFrame:
from gsalib import GatkReport
report = GatkReport('/path/to/gsalib/test/test_v1.0_gatkreport.table')
table = report.tables['ExampleTable']
https://gsalib.readthedocs.io/en/latest/
- Issue Tracker: https://github.com/myourshaw/gsalib/issues
- Source Code: https://github.com/myourshaw/gsalib
The project is licensed under the MIT license.