esvee v1.0-rc.2

Config:

• optionally set 'frag_length_file' for Assembly and Caller, otherwise continues to assume file is named TUMOR_ID.esvee.prep.fragment_length.tsv

sage v4.0-rc.2

Technical:

• expand BAM sampling for read length to test all panel regions with buffer

teal v1.3.2

Technical:

• uses BamMetrics summary file

virus-interpreter v1.7-rc.2

Technical:

• Re-trigger failed docker image build

virus-interpreter v1.7-rc.1

Technical

• uses BamMetrics summary file

v-chord v1.0

Initial release

sage v4.0-rc.1

BQR

• Round consensus BQ to canonical quals and 1
• Increase min mapping quality for BQR from 10 to 50, and change AD/AF site thresholds
• Handle contexts with 0 identified errors
• BQR by consensus type
• Update error rate calculation to be robust to different qual distributions per-base

Read context & evidence counting

• New read context algorithm
• Changes to read context annotation
• New read counting conventions
• Approximate ref matching logic for long inserts
• Allow SNV/MNV support in soft-clips
• Fragment sync prefers aligned over non-aligned base quals

Qual model

• Qual filter dynamically scales with depth and splits map and base qual tests
• Explicit germline mode which incorporates empirical VAF implausibility into model
• Novel indel qual is conditionally boosted
• Changes to high depth mode
• Modify edge penalty more in line with realised error rates, and facilitates partial core qual contribution
• Use min base qual rather than mean base qual for MNVs
• Indel qual for MSI repeats is based on microsatellite empirical qual
• Jitter penalty model is overhauled

Filtering

• MED based on distance to soft clip instead of distance to end of read
• MED uses max per-read edge distance for fragments with overlap
• MED uses max edge distance across depth-supporting reads, not just ref
• MAX_READ_EDGE_DISTANCE_PERC split between panel and non-panel regions
• Fix dedupMnv bug
• Filter if ALT average fragment length << REF average fragment length
• Filter if portion of realigned read support for short indel is unusually high
• Filter at candidate phase if only one distinct fragment provides support
• Min fragment coordinate check is stepped and applies all the time
• Tumor VAF filter now uses recalibrated qual

Config:

• msi jitter files mandatory unless 'skip_msi_jitter' specified. Uses BAM path if 'jitter_param_dir' isn't specified

redux v1.0-rc.1

Functional

• write MSI jitter files for Sage
• unmap secondaries and drop from BAM
• use median base qual from selected consensus base
• no dual fragment marking if not duplex UMIs
• drop supplementaries with alignment score < 30 (BWA default)

Technical

• handle hard-clipped reads
• minor memory and performance optimisations

Bugs
-unmap read in unmap region if map becomes unmapped and vice versa

• rare repeated writing of supplementaries

purple v4.1-rc.1

Functional

• biallelic model changes
• somatic readjustment model in tumor+reference mode
• updated rules for somatic fit and no-tumor classification in tumor-only mode
• restrict somatic variant plotting to target regions only when enabled
• germline chromosomal aberrations support TRISOMY_9P and TERTRASOMY_9P
• SV recovery removed
• disable whole genome dup check for tumor-only non-normal fits
• removed VAF bounds check on hotspots for somatic fitting
• remove indel repeat count from TSG reportability check
• VAF 2% filter for tumor and MSI load
• tumor-only and targeted fits ignore diploid status, no reversion from deleted genes
• VAF threshold 35% to use non-hotspot variant in tumor-only fit
• revert germline adjusted CN change to JCN if not fitted region match found
• fixed germline deletion exon boundaries

Technical

• compatible with Esvee
• removed HRD output from standard run
• calculate target region coding base total using Ensembl instead of CODING tag from BED file
• write empty files on empty/invalid inputs

Bugs

• germline deletion avoid use of next region's min start

pave v1.7-rc.1

Functional

• allow reporting of indels in repeats of length > 7
• changes to PON filtering rules based on hotspot status, Gnomad, VAF and PON sample counts

Technical

• changed impact canonical gene name variable to gene name

Config

• germline to skip gnomad filter use config 'gnomad_no_filter'

PON Building

• PON builder uses 40 for default qual cut-off
• remove Pathogenic/Likely Pathogenic variants from 37 & 38 PONs