morinkit

Python functions for cancer genomics


Keywords
bioinformatics, cancer, genomics, utility, tool
License
GPL-3.0
Install
pip install morinkit==0.1.1

Documentation

Morinkit: Python functions for cancer genomics

PyPI Build Status Coverage Status

Morinkit is a Python package that bundles several functions meant for cancer genomics. Examples include:

  • ensemble_vcf: Perform ensemble SNV calling by integrating VCF files generated by different methods.
  • augment_maf (coming soon): Annotate a MAF file with the allele counts from various BAM files.

Installation

You need Python 3.3 or later to install morinkit.

pip install numpy Cython  # Or `conda install numpy Cython`
pip install morinkit

Dependencies

  • Python 3.3 or later
  • cyvcf2

Functions

ensemble_vcf: One of the ICGC-TCGA DREAM challenges showed that ensemble SNV calling led to the highest accuracy (doi:10.1038/nmeth.3407). Ensemble_vcf is primarily meant to integrate the VCF files from different methods and only output variants supported by some number of methods (or fraction of methods).