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

orange v3.7.1-rc.1

Functional:

• add presence of tumor stats to quality control page and to orange-datamodel
• ensure only exonic variants that are phased with reported variants are shown in 'potentially interesting' section
• add potentially interesting chromosomal rearrangements (1q trisomy and 1p19q co-deletion) to report
• derive breakend fields type, chromosome, chromosomeBand, orientation and junctionCopyNumber from root sources

Technical:

• use BamMetrics summary and flagstat data

linx v2.0 release candidate 1

Functional

• write inexact homology to germline disruption file
• germline report DELs and DUPs in complex clusters if < 3M in length
• use JCN as last factor in in fusion priority

Technical

• compatible with Esvee, does not support Gridss
• visualiser: set white background for chr band and fusions
• visualiser: limit plot SV count to 2K, can override with 'max_plot_svs', zero allows any count

health-checker v3.6-rc.1

Technical

• uses BamMetrics summary file and flagstats

esvee v1.0-rc.1

Initial release, see READ-ME for full details

cobalt v2.0-rc.1

Technical

• handle missing ratio results from empty BAM
• ensure target regions file is sorted

chord v2.1-rc.1

Technical

• code refactor

bam-tools v1.3 release candidate 1

Functional:

• count overlapping bases towards standard coverage
• allow reads partially overlapping a targeted region in target-only mode

Bugs:

• fixed tracking of consensus reads for coverage, counts and fragment lengths

Technical

• write partition statistics
• removing writing of old-style metrics file

amber v4.1 release candidate 2

No changes for WGS

Bugs:

• fixed restriction to panel regions in targeted mode

cuppa v2.3.0

Technical

• introduce Java entry point for prep + prediction
• compatible with Esvee

Bugs

• fix misalignment of cancer type in visualisation