gsalib: Python/pandas package of utility functions for GATK¶
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.
Features¶
- 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
Example¶
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']
Documentation¶
Contribute¶
- Issue Tracker: https://github.com/myourshaw/gsalib/issues
- Source Code: https://github.com/myourshaw/gsalib
License¶
The project is licensed under the MIT license.