UGA GACRC Sapelo2 specific script to call variants amongst samples of bacteria pathogens. Download/clone the repository in the working directory where your samples are located and run the program as instructed here.
FASTQ samples -> Trimmed FASTQ, BAM files, VCF files, RAxML tree, Alignment Stats, Genome Annotation file.
running with bash:
bash ./bacteria_SNP/bacteria_pathogen_SNP.sh /path/to/ref.fa email address
running on sapelo2 cluster:
qsub -v "reference=/path/to/reference.fa,email=email@uga.edu" ./bacteria_SNP/bacteria_pathogen_SNP.sh
To check on your output, just move into the output_dir/ directory!
further documentation on output is found in the file 'BacteriaSNP.docx'