The following tools are required.
BBMap from [BBTools](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/)
Samtools
Picard
BWA
[Jvarkit](https://jvarkit.readthedocs.io/en/latest/)
Snakemake
FASTQ reads in this repo were generated synthetically with ArtificialFastqGenerator to avoid using human identifiable data.
This was the command used to generate read data from the HLA-A Ensembl gene reference sequence.
java -jar ArtificialFastqGenerator.jar -R Homo_sapiens_HLA_A_sequence.fa -O HLA -S ">6" -TLSD 10 -X 10 -RL 100 -TLM 300 -URQS true -SE true -F1 test1.fastq -F2 test2.fastq