Include SVs into somatic report configuration.

[axelgschwind]

Currently, somatic structural variants are chosen by hand.

Like germline SVs, somatic SVs should be imported into NGSD and the user should be able to select a SV for the somatic report configuration.

[Ott-Alexander]

• [ ] Config fields for somatic SV-config - exclude reasons [artefact, unclear effect, other], description, comment, overwrite fields (of germline), rna information [confirmed, not confirmed, RNA data not usable]

• [ ] Create tables in NGSD

• [ ] add import option for somatic SVs to NGSDAddVariantSomatic

• [ ] GSVar: improve SV-Widget for somatic

  • [ ] target region filter auch auf Breakpoint_Genes anwenden (basierend auf Gennamen, automatisch von kleinen Varianten übernehmen)
  • [ ] additional infos at the bottom
    • [ ] provide exon/intron + number (x/y ?) and domain information for breakpoints if possible
    • [ ] genes at Breakpoints - if genes are on 3' or 5' strand, with tsg, oncogene and link to genome nexus
    • [ ] The SV type (BND, DUP, DEL, ....), SomaticScore, the 4 Tum_PR/SR_ref/alt, Flags,

• [ ] Report: add table to somatic report (see Sorin E-Mail from 14.03.24)