seqCapture

Bioinformatic workflow for analyzing sequence capture NGS dataset

Install:

1. Obtain the latest version of seqCapture:

     $ git lfs clone https://github.com/CGRL-QB3-UCBerkeley/seqCapture.git
   

2. Download your own GATK. You will need to register and log into the GATK to access the download. Place your GenomeAnalysisTK.jar to the diretory "seqCapture/dependencies/morePackages":

     $ cp /path/to/GenomeAnalysisTK.jar  seqCapture/dependencies/morePackages
   

Note that in the next update, GATK will not be used any more as realignment around indels is no longer available for GATK4.

3. Install Miniconda2. NOTE: the current version only supports Miniconda2 (Python2.7) but it is pretty easy to make a Miniconda3 (Python 3) compatible version. If that is what you need, please contact the author.

     $ bash Miniconda2-latest-xxxx-x86_64.sh
   

4. Install seqCapture:

     $ cd seqCapture/
   

   4.1 for MacOS users:

     $ ./install_osx64.sh
   

   4.2 for linux users

     $ ./install_linux64.sh
   

Uninstall (which is sad):

     $ cd seqCapture/

     $ ./uninstall.sh

Use seqCapture:

1. Activate the conda environment

     $ source activate seqCapture
   

   Note: to deactivate an environment, run "source deactivate"

2. Print out all seqCapture commands

     (seqCapture) $ seqCapture
   

Contact:

Ke Bi: [email protected]