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