sage v3.4 release candidate 1

Functional

• sync overlapping fragments on by default
• sync overlapping fragments logic: favor longer INDELs for CIGAR mismatch, forms consensus no matter how many bases are mismatching, ignore 3’ side of overlap where insert size < read length
• VCF writes AMQ (average map qual), ANM (average events per read) and MED (max edged distance)
• soft-filter average map qual for ref vs alt reads if different > 15
• average base qual filter lowered from 28 to 25
• new modMAPQ logic supports calling low mapq regions (default behaviour unchanged)
• added read strand bias filter
• added maxEdgeDistance filter
• AF filter can pass with lower AF if p-value condition met
• new deduplication logic for INDELs logic handles 1:M deduplication

Targeted panel mode, enabled with config 'high_depth_mode':

• ignore all reads with AD<30
• ignore all soft clip support
• added jitter AF filter
• BQR ignores overlapping bases

Bugs

• fragment strand bias calculated incorrectly

HTML Visualisations added for variants:

• creates a HTML for a subset of variants based on config. Shows read context and fragment support
• config 'vis_variants' to specify variants to produce visualisations, format: 'chromosome:position:ref:alt' separated by ';'. Will only run sage for +/- 200 base region around specified variants.
• config 'vis_pass_only' to generate files for passing variants, must be called with 'specific_regions'
• config 'vis_output_dir' default 'vis' if not specified

Config:

• sync_fragments removed since now on by default. Use 'no_fragment_sync' to disable.
• output -> output_vcf

pave v1.6 release candidate 1

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

cobalt v1.16 release candidate 1

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

wisp v1.1 release candidate 1

Functional:

• improved copy number plots
• somatic VAF ratio peak plots
• probe selection second pass with lower limits
• probe selection with lower GC and fragment limits, using raw AF and allow no Linx directories

Technical:

• handle synthetic tumor variants, ie purity estimation without tumor pipeline Purple results
• annotate with probe variants and handle batch control samples if available

Config:

• gc_ratio_min now required (set 0 for WGS, 0.4 for targeted-panel)

pave v1.5.1

HGVS coding for duplications now uses duplicated base positions instead of variant position

patient-db v5.34 rc1

Preliminary release of v5.34

teal v1.2.1

Minor update:

• fix backward compatibility issue with cobalt gc median file

purple v4.0 rc1

Functional:

• don’t fit short arms on 13,14,15,21,22
• Mask IG/TCR regions in fit
• Mask regions <2MB from centromere in fit
• Where ambiguous (low purity), BAF is now fit to minimise major allele CN
• chromosome X CN amplifications are called at 1.5x ploidy for males
• don’t smooth large germline deletions in diploid normalisation logic
• fit in 0.5% intervals for purity <20% and lower min to 7%
• write list of reportable transcripts to somatic VCF when alt-transcripts (eg CDKN2A) exist for a driver gene
• add LOH percent to QC output file

Technical:

• allow extra sample IDs in VCF and any order
• throw exception and exit on charting error

Bugs:

• ploidy was not calculated accurately in somatic mode

Visualisations

• only show diploid regions in input.png
• tumor is always in blue in input.png

Panel:

• add deviation penalty adjustment for GC ratio (config: gc_ratio_exponent, deviation_penalty_gc_min_adjust)
• set targeted panel default values:
  -ploidy_penalty_standard_deviation 0.10
  -ploidy_penalty_min 0.20
  -ploidy_penalty_sub_one_major_allele_multiplier 3.00
  -deviation_penalty_gc_min_adjust 0.25
  -gc_ratio_exponent 3.0
  -min_diploid_tumor_ratio_count 3
  -min_diploid_tumor_ratio_count_centromere 3

gripss v2.4.rc1

Technical:

• handle Gridss VCF with sample IDs in reversed order

Panel:

• added panel soft filters: qual-per-AD and modified AF
• set panel config by default if in target regions mode
  -hard_min_tumor_qual 200
  -min_qual_break_point 1000
  -min_qual_break_end 1000
  -filter_sgls
  -qual_per_ad 30
  -modified_af 0.03
  -modified_af_hotspot 0.005

teal v1.2.0

• Update to match cobalt v1.16+.
• Use mean read depth and gc50 read depth instead of read count per 1000 bases window.
• removed reference / tumor mean_reads_per_kb and gc50_reads_per_kb command line arguments in standalone mode.
• added reference / tumor mean_read_depth and gc50_read_depth command line arguments in standalone mode.