morinlab/morinkit

Name: morinkit

Owner: Ryan D. Morin Laboratory

Description: Python functions for cancer genomics

Created: 2016-07-27 19:50:25.0

Updated: 2016-12-06 18:30:52.0

Pushed: 2016-12-07 05:57:58.0

Homepage:

Size: 56

Language: Python

GitHub Committers

User	Most Recent Commit	# Commits
Bruno Grande	2016-12-07 05:49:08.0	9
rdmorin	2016-12-06 18:30:51.0	1

Other Committers

User	Email	Most Recent Commit	# Commits

README

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.

Installation

You need Python 3.3 or later to install morinkit.

install numpy Cython  # Or `conda install numpy Cython`
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).