v1.1

Nextflow pipeline to predict neoantigens from WGS data.

1. Extract reads associated with the MHC region directly from CRAM/BAM files.
2. Support HLA genotyping for both class I and II HLA genes (xHLA).
3. Annotate the impact of point mutations using Gencode V33 (VEP-ensembl) and remove VAF from the VCF file.
4. Predict neoantigens using an ensemble of methods for both classes and predictions are filtered using standard cutoffs (pvacseq).