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ScanNeo2 v0.2.0
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@riasc riasc released this 01 Mar 04:10
· 59 commits to main since this release
v0.2.0
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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)
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