sage v4.0-rc.4

Functional:

• panel max germline VAF use adjusted limit for a single ref read

redux v1.1-rc.3

Technical:

• optimised UMI collapsing across multiple duplicate groups
• optimised MSI jitter analysis
• optimised BAM writing

purple v4.1-rc.3

Functional:

• cap inferred SV copy number at 1000
• improve somatic fit diplod purity matching

esvee v1.0-rc.6

Functional:

• Prep keep discordant-only remote junctions, prioritise over split if split support is below minimum
• classify duplicate-orientation fragments as discordant
• disc-only pair assembly link requires only 20 bases of overlap
• Caller checks exact reference sample nome to mark as germline

purple v4.1-rc.4

Description of release purple v4.1-rc.4

Full Changelog: cuppa-v2.3.1-rc.3...purple-v4.1-rc.4

teal v1.3.3

Bug fix:

• Fix bug where telomere length is set to NaN if no telomeric read is found.

redux v1.1-rc.2

Technical:

• Replace sambamba with samtools in Dockerfile

redux v1.1-rc.1

Bugs:

• fixes a couple of minor & rare issues which could result in either dropped or duplicate reads

Technical:

• has significantly lower memory usage

Config:

• requires samtools instead of sambamba for final BAM concatenation

esvee v1.0-rc.5

Functional:

• cap frag distribution output by max observer read length, to avoid use of short adapter-trimmed reads

Technical:

• load disc stats file from prep dir instead of output dir

cuppa v2.3.1-rc.3

Technical:

• Fix bug where RNA classifier probs were shown when RNA data is missing. This was due to MissingFeaturesHandler erroneously filling in NAs for samples with no RNA data