v3.0.0, reduced i/o

3.0.0

• Germline bed file is now merged for adjacent regions (#31)
• Ability to use fragment based counts for filters (#56)
• More compressed intermediate files (#55)
• Change to Const::Fast where appropriate (#41)
• Removed TG VG from genotype.
  • Readgroups are always variable, often 1 in data from last few years
  • Not used by our filters.
• Supports BAM/CRAM inputs
• Output will be aligned with inputs
  • bam vs cram
  • bai vs csi
• Although ground work for csi input/output has been done Bio::DB::HTS doesn't support csi indexed input yet.
  • Created our own fork at cancerit/Bio::DB::HTS so that this could be enabled.
  • You will need to install this manually or use one of our images for this functionallity.
    • dockstore-cgpwxs
    • dockstore-cgpwxs