Python GATK Autorun

This Python script uses the tk GUI to help automate a run of genomic analysis.

This software is designed to perform a run from pure reads (.fasta and .fastq files) through all of BWA and preprocessing using SAM and Picard tools. Finally this will allow you to run GATK as well as multiple realignments around indels for purifying SNP reads.

--------------------------------------------

Major Updates:

-August 8th, 2014
Initial upload of file, currently BWA functions should be working, but there is no guarantee that the produced SAM file is correct at this time.

-August 12th 2014
Reorganized class files in to seperate files, add source code directory, cleaned up UI and added sleectable output directory. Still only able to handle BWA steps.

--------------------------------------------

This software is open source and free to use by anyone. If you wish to provide a modified version of this software please provide credit to Dylan Lawrence (dlawre14@slu.edu) for the original program. 

--------------------------------------------

For any questions please email dlawre14@slu.edu

--------------------------------------------

To Do List:

-Add documentation and clarity to files
-Modify directory selector to allow for creation of directories