Pynnotator
==========

A Python Annotation Framework for VCF files (Exome or Genome) from
Humans using multiple tools and databases.

Libraries
=========

-  htslib (1.3.1)
-  vcftools (0.1.14)
-  snpeff (SnpEff 4.3)
-  vep (version 84)

Databases
=========

-  1000Genomes (Phase 3) -
   ALL.wgs.phase3\_shapeit2\_mvncall\_integrated\_v5b.20130502.sites.vcf
-  dbSNP (including clinvar) - (human\_9606\_b147\_GRCh37p13)
-  Exome Sequencing Project - ESP6500SI-V2-SSA137.GRCh38-liftover
-  dbNFSP 3.2a (including dbscSNV 1.1) -
-  Ensembl 84 (phenotype and clinically associated variants)

Features
========

-  Multithread Efficient
-  Annotate a VCF file using multiple VCFs as a reference

Requirements
============

-  Ubuntu 16.04 (probably also works on 14.04)
-  Python 3.4+
-  At least 40GB

Installation
============

::

    mkvirtualenv -p /usr/bin/python3 pynnotator
    pip install cython 
    pip install pynnotator
    pynnotator install
    

Test
====

::

    pynnotator test