HLA pipeline release

• Replaced Annovar by VEP
• Replaced epitope generation function by Varcode
• Use only Ensembl to annotate and compute epitopes
• General bug fixes and improvements

HLA pipeline release

• Added flag to disable Spark
• Optimized the parallel code
• General improvements and bug fixes

HLA pipeline release

• Fixed small bugs in merge_results.py

0.6.1

• Spark is now disabled by default in GATK
• Few small improvements

HLA pipeline release

• Improved the generation of epitopes

HLA pipeline release

• Improved epitope generation function
• Added OptiType for HLA typing
• Added logging
• Added QC steps (BAM, FASTQ and VCF)
• Added multi-processing
• Added more fields in merge_results.py
• General improvements and bug fixes
• Added option to use intervals for exome data

HLA pipeline release

• Better QC
• Fix small bugs in merge_results.py

HLA pipeline release

• Added intervals to Strelka2 and Varscan
• Fixed minor bugs

HLA pipeline release

• Better naming and docs
• Parallelize some part of the workflows
• Minor bugs and improvements
• Added QC steps (FastQC and BamQC)

HLA pipeline release

• Refactored the computation of epitopes
• Simplified the workflow of the pipelines
• Refactored merge_results.py
• General improvements and bug fixes