/SVAFotate

Annotate Structural Variants with Population Allele Frequency Info

Primary LanguagePythonMIT LicenseMIT

SVAFotate

Annotate Structural Variants with Population Allele Frequency Info

SVAFotate repository has moved:

The main SVAFotate repo has been moved to here.

Please use the new SVAFotate repo.

This repo is deprecated.

Installing SVAFotate

  1. Installing Miniconda
  • If Miniconda is not installed on your system, install it from miniconda
  1. Set up new conda environment
$ conda create --name svafotate-env python=3

$ conda activate svafotate-env
  1. Install package requirements
$ conda install --file https://raw.githubusercontent.com/mikecormier/SVAFotate/master/requirements.txt?token=AIM3FBTOHCDMZJYYLOX3OYC7B7FGW
  1. Install SVAFotate
$ pip install -U git@github.com:mikecormier/SVAFotate.git
  1. Check that SVAFotate installed Correctly
$ svafotate --version

svafotate 0.0.1

$ svafotate -h 

usage: svafotate [-h] [-v] {annotate,pickle-source,custom-annotation} ...

SVAFotate: Structural Variant VCF Annotation tools
==================================================

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         Installed version

[sub-commands]:
  {annotate,pickle-source,custom-annotation}
    annotate            Annotate SV VCF File
    pickle-source       Pickle Source Bed
    custom-annotation   Add custom annotation(s) to source annotation file