ScanNeo2 v0.3.0

Features

• Added sequence similarity filter for MHC-I
  • self-similarity (using kernel similarity)
  • pathogen similarity (BLAST against pathogen-derived epitopes from IEDB)
  • proteome similarity (BLAST against human proteome)
• Prioritization of neoantigens is now done separately for each variant type (speeds up the process)
• Update to recent version of ScanExitron (Thanks to @dolittle007)
  • this version updated to recent version of regtools (v0.5.0) - which is available on Conda
  • Singularity/Docker is not necessary anymore
  • Added option to use strand information in exitron calling
• ScanNeo2 now uses conda environments for all tools (ditched Singularity/Docker)

Fix

• renamed similarity fields for pathogen and protein to more descriptive names

ScanNeo2 v0.2.12

Fix

• Fixed missing alleles in HLA alleles reference list - #34

ScanNeo2 v0.2.11

Fix

• Updated transindel environment to recent samtools version (as --o introduced in samtools >= 1.13 required by transindel)

ScanNeo2 v0.2.10

Fix

• Force combining multiple VCF files in indel detection using mutect2 (e.g., when multiple samples are provided)

ScanNeo2 v0.2.9

Fix

• Splitted rules in HLA typing to ensure better distribution of the workload
• Changed order in HLA typing rules (BAM files are now part of single-end)
  • samtools fastq is only called for BAM files
  • input of filtering directly from preprocessed/raw reads

ScanNeo2 v0.2.8

Fix

• Added threads option to samtools sort calls to speed up the process
• Fixed wrong call to optitype within the wrapper script

ScanNeo2 v0.2.7

Fix

• Separated samtools, bcftools and realign environments to avoid conflicts
• Changed order of genotyping rules to catch errors when no alleles can be found
  • Alleles are merged according to nartype (e.g., DNA, RNA) and then combined
• Force concat of VCF files in genotyping to avoid errors when no variants are found
• Added optitype wrapper to avoid errors when empty BAM files are provided / no HLA reads

ScanNeo2 v0.2.6

Fix

• Added routines to catch errors when rnaseq data is not provided but exitron/alternative splicing calling is activated
• Added reference genome index as input to germline indel calling (necessary when only indel calling is activated)
• removed -C from BWA mem call (on DNAseq data) to avoid error on Illumina identifiers

ScanNeo2 v0.2.5

Fix

• Wrong indentation in HLAtyping caused error when providing no normal sample (NoneType was being iterated)
• Fixed missing input in get_reads_hlatyping_PE rule (tmp folder) that caused error when using paired-end reads
• Added else case in get_input_hlatyping function (rule get_reads_hlatyping_PE) for input reads when preproc is deactivated

ScanNeo2 v0.2.4

Fix

• Added concurrency to splAdder call
• Added routines that lets ScanNeo2 finish (even when splAdder results are empty or faulty)