sequencing/ant-tools

ant-tools
=========

ant-tools facilitates the extraction of variant annotation from the .ant files produced by Illumina sequencing applications.


Requirements:
git
Python 2.7

Build Requirements:
mono (including source)
glibc

Recommended System Requirements:
> 8GB RAM

Usage:

  ant-tools.py antFileName [--validate] [--stats] [--all] [--bedout] [--range=RANGE] [--bed=BED_PATH]
  
  antFileName: the fully qualified path to the .ant file.
  
  Options:
    --validate: validates that the ANT file is in the correct structure.
    --stats: provides a summary of annotation version, contents, etc.
    --all: specifies that empty records (i.e. no annotation) should be included in the output.
    --bedout: specifies that the output should be BED-like in format, i.e. CHROM	START	STOP	{JSON_DATA}
    --range=RANGE: allows the specification of a range over which to dump annotations, where RANGE is: CHR:START-STOP.
    --bed=BED_PATH: specifies an input BED file indicating the regions for which to export annotation.
    
    
Installation:
From a command prompt:
git clone https://github.com/sequencing/ant-tools


ant-tools ships with precompiled binaries for major Linux distributions.  If a binary does not exist or is incompatible with your distro, you must manually build ant-tools.

Build Instructions:
  - If you don't already have a working mono dev env, download and install the mono MDK from http://www.mono-project.com/download/
  - depending on your environment, you may need to update build.sh so that MONO_SOURCE_DIR reflects your environment.
  - from a command prompt, execute:
    git clone https://github.com/sequencing/ant-tools
    cd ant-tools
    source build.sh