Instillation and Requirements

Install LoFTK

The scripts will work within the context of a certain Linux environment - in this case we have tested LoFTK on CentOS7 with:

1. Simple Linux Utility for Resource Management (SLURM). To clone LoFTK for SLURM (default:master):

git clone https://github.com/CirculatoryHealth/LoFTK.git

2. Sun Grid Engine (SGE). To clone LoFTK for SGE:

git clone -b LoFTK_SGE https://github.com/CirculatoryHealth/LoFTK.git`

Requirments

• Perl >= 5.10.1`

• Bash

• Ensembl Variant Effect Predictor (VEP)

  See documentation for full installation instructions.

  • Additional CPAN modules

    The following modules are required to use VEP along with LOFTEE.

    • DBD::mysql - required for database access (--database or --cache without --offline)
    • Bio::DB::BigFile - required for reading custom annotation data from BigWig files

• LOFTEE

We recommend you to download LOFTEE that corresponded to your data Genome assembly (GRCh37 or GRCh38)

1. LOFTEE for GRCh37 The following files are required to be downloaded.

   • Ancestral sequence (human_ancestor.fa[.gz|.rz])
   • PhyloCSF database (phylocsf.sql) for conservation filters

2. LOFTEE for GRCh38 The following files are required to be downloaded.

   • GERP scores bigwig (gerp_bigwig)
   • Ancestral sequence (human_ancestor_fa)
   • PhyloCSF database (loftee.sql.gz)

• samtools (must be on path)

To export the path of samtools to your shell PATH, you need to execute the following command:

$ export PATH=/directory_to_your_samtools/:$PATH

or you can insert the command above in your .bash_profile or .bashrc in you home directory.