cobalt v1.16

Functional:

• add referenceGcContent and tumorGcContent outputs
• use mean read depths instead of read counts, and change GC normalisation to use median instead of interpolated median

cider v1.0.3

Technical:

• handle unpaired reads

amber v4.0

Functional:

• default min map quality now 50 from 1
• disable min/max depth checks in target-regions mode
• min tumor default (config: tumor_min_depth) defaults to 25 for tumor/normal, 8 for tumor-only
• restrict sites to target regions in panel mode

Config:

• target_regions_bed - provide this file in targeted panel mode

neo v1.2 beta

Config:

• optionally specify RNA Sample Id with -rna_sample. Neo will then expect this RNA sample ID to have been used for Sage Append and in the Isofox file names (TPM and neoepitope RNA annotation).
• req_amino_acids - defaults to 15 for both generator and scorer routines

pave v1.6

Functional:

• keep splice effect for any phased variants
• HGVS coding for dups now shift position to duplicated bases
• handle phased missense and synonymous protein impacts
• phasing check for SNV/MNV overlap with inframe INDEL separately from frameshift count 2+
• favour protein duplications over inserts when considering realignment
• use stop-gained in HGVS protein instead of frameshift if has both

Bugs:

• check ref codon bases are valid in phasing routine, could cause crash if variant was at very end of exon with open reading frame
• fixed ref codon addition for overlaps in phasing logic

Technical:

• exit on thead error
• multi-threaded

Config:

• threads (default 1)
• removed gnomad_load_chr_on_demand

linx 1.25

Functional:

• check IG breakends in SGL mappings for fusions
• dedup matching IG fusions
• IG enhancer fusions ignore proteins lost for 3' gene
• fixed protein feature required start for downstream transcripts

Technical:

• set VCF genotype ordinals from sample ID
• set driver category from driver gene records

orange v3.1.0

• ORANGE report now shows the new CUPPA v2.0 visualization
• New ORANGE-datamodel (v2.2.0) supports the tabular output from both CUPPA v2.0 and CUPPA v1.x
• :: is used rather than _ to concatenate the two genes fused in DNA and RNA fusions (impacting orange-datamodel!)

crest v1.0.0

Initial release of Crest, a tool that checks that WTS samples are correctly matched to the same patient as the WGS sample.

compar v1.2

Functional:

• detailed Lilac frag count checks
• filter for PASS status when reading germline variants from file

Technical:

• split Chord and CUPPA mismatches into separate files

sv-prep v1.2.3

Bugs:

• set AF using BVP only if SGL
• retain existing junction status when registering junction fragments