esvee v1.1-beta.4

Description of release esvee v1.1-beta.4

Full Changelog: gene-utils-v1.2...esvee-v1.1-beta.4

esvee v1.0-rc.8

Bugs:

• apply ref-base check for local indel-type assembly links with exact sequence matches

gene-utils v1.2

Functional:

• fusion generation - add support for new 38 columns in knowledgebase sheet

Technical:

• region file validation preserves additional fields, handles headers and non-BED files

esvee v1.0-rc.7

Functional:

• cigar indels alignments skip map qual tests
• Caller: ignore chained status for min avg length filter
• increase BWA mismatch and gap open penalty by 2
• hotspot min junction read count 2 -> 1 (to match capture in Prep)
• alignment score threshold 0.85 -> 0.77
• require standard overlap around junctions to merge phase set assemblies
• extend seeded matched assembly sequence to find maximum match
• Prep: discordant junc remote read count always set
• Prep: ensure low-base-qual supplementaries are kept for discordant groups

Bugs:

• fixed local indel fragment length calc
• prevent links between INDEL and non-INDEL assemblies

amber v4.1-rc.3

Functional:

• modified contamination check conditions to consider low-VAF peak and any number of sites with 3+ reads

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

Technical:

• Re-triggered cloud build to build docker image which failed in purple-v4.1-rc.3