These scripts automate the analysis of the data of the Genetics of Race project for the BioSeq project. The use a config file that is specified in the genRaceAnalysis.py script. The join2Fastas2.py script is used by the aforementioned script as a helper procedure. A sample config file is included. It has several fake entries to demonstrate that the program can handle bad input.

Author: Philip Braunstein Contact: pbraunstein12@gmail.com

=========== CONFIG FILE

This script uses a CONFIG file that specifies that lists the HVRI vcf file then the HVRII vcf file from the same sample on each line. The names on each line are comma-speparated. Each name is listed without the .vcf extension. So, if the vcf file is S501N703_S11.vcf, the CONFIG file lists this as S501N703_S11.

The path to the CONFIG file is specified in the CONFIG constant at the top of this file.

============= DEPENDENCIES

1. Path to the GATK jar file must be in the GATK constant. It is easiest
   to have a sym link in the directory.
2. Path to the join script must be specifed in the genRaceAnalysis.py. 
   Likewise, it is easiest to have this script in the same directory.