The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
T1Kfor DNA HLA typing aside from OptiType.- Now proximal variants are reported on a per variant basis using
pysam
yaramapnow usessamtools collateandsamtools fastqto generate the intermediate gzipped fastq to feed into yara mapper. Intermediate files are not removed.VEPnow generates a bgzipped and tabix indexed VCF.
Fastpfor trimming and quality control of input FASTQ.arcasHLAadded for typing and expression of HLA alleles in RNA.
trim_galoreandFastQChave been replaced withfastpOptiTypehas been removed forneopredrnaand replaced witharcasHLAVEPandpyensemblbumped from version 104 to 109.