Linx 1.11

Functional:

• uses driver gene panel with reportable disruptions to report homozygous disruptions and disruptive breakends
• resolved pairs cannot be interrupted by non-simple, non-contained SVs
• satellite SGL merge requires same arm
• disallow single-cluster DELs from being AMP candidates

Fusion changes:

• see Linx documentation for full details
• mark some 3’ promiscuous as high-impact
• report promiscuous fusion in known exon ranges
• replace phased column with INFRAME, SKIPPED_EXONS or OUT_OF_FRAME
• write a likelihood column: HIGH if known, IG known, exon del-dup or promiscuous exon, othereise LOW or NA is not reported
• set exons skipped to zero for exonic breakends
• allow chain terminated for IG known pair and exon del-dups
• exon DEL-DUP fusions now allow exon skipping
• support alternate mapping for known and IG-region fusions
• allow SGL to use alt mappings without QualScore specified

Latest HMF fusion reference data is attached.

Bugs:

• re-test cluster-merge by foldbacks after final chaining for non-assembled chained foldbacks

Technical:

• loads driver gene panel from file (-driver_gene_panel)
• allow chain-terminated non-known fusions to be loaded tp DB and written to file (but still not reportable)
• removed support for old-style fusion reference files (fusion_pairs_csv, promiscuous_five_csv and promiscuous_three_csv)

DB changes:

• see patient-db linx 1.11 patch for svCluster and svFusion table updates