Morinkit: Python functions for cancer genomics
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.
You need Python 3.3 or later to install morinkit.
pip install numpy Cython # Or `conda install numpy Cython` pip install morinkit
- Python 3.3 or later
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).