ScanNeo2 v0.2.3

Features (somewhat)

• Added paramter nonchr in reference attribute to exclude non-chromosomal contigs from the reference genome

Fix

• Fixed wrong path in quality control for single-end reads

ScanNeo2 v0.2.2

Fix

• Updated spladder env to ensure that install wheel works (pysam requires python 3.6)

ScanNeo2 v0.2.1

Fix

• Removed hlahd path from config and hlatyping - needs to be installed in $PATH

ScanNeo2 v0.2.0

Features

• ScanNeo2 supports Snakmake>=8
  • --use-conda replaced by --software-deployment-method conda
  • --use-singularity replaced by --software-deployment-method apptainer
• Gather/scatter of the indel calling speeds up ScanNeo2 on multiple cores
  • added script to split bamfiles by chromosome (scripts/split_bam_by_chr.py)
  • haplotypecaller first/final round is done per chromosome and later merged
  • mutect2 is done per chromosome and later merged
• Genotyping MHC-II works now on both single-end and paired-end
• User-defined HLA alleles are matched against the hla refset
• Added multiple routine to catch errors when only custom variants are provided
• Added additional parameters in config file

Fix

• When using BAMfiles the HLA typing wrongly expected single-end reads and performed preprocessing
• Each environment is no thoroughly versioned to ensure interoperability
• Missing immunogenicity calculation on certain values of MHC-I fixed
• Fixed prediction of binding affinity in MHC-II (as the columns are different from MHC-I)

ScanNeo2 v0.1.6

This release includes a small fix in which the prediction tools (e.g., binding affinity/immunogenicity) are additionally linked as input to the prioritization. This enables more flexibility in the order of the rules.

ScanNeo2 v0.1.5

Small fix that replaces custom reference to global used ENSEMBL reference genome.

ScanNeo2 v0.1.4

This release includes a small fix when snakemake first executed the exitron calling. The annotation was unavailable (as other rules had to be called first).

ScanNeo2 v0.1.3

This release adds subroutines/fixes when no normal samples (in the config) are provided. ScanNeo used to abort when this is left empty due to a comparison with NoneType.