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CHANGELOG

v2.0.7

  • Changed the default reference genome for CNV calling from unmasked hg38 to hg38 with masked regions. CNV calling now uses the masked hg38 reference by default.
  • Fixed the missing "-wgs" suffix in the GENS load command by appending it to the case/group id ("--case-id"), when needed.

v2.0.6

  • Fixes automatically different illuminia platforms based on the csv information
  • Updated the PONs for the cnv from NovaseX
  • Support for gene fusions from duplication and deletion events in the fusion calling.

v2.0.5

Hot fix the vep gnomad filter

  • Updated and pushed fix_vep_gnomad.pl script to fix the gnomad filter for vep annotations

v2.0.4

Hot fix finding missing fusion in Solid panel

  • Updated the filter_with_fusion_panel.pl script to read panels with geene2 missing.

v2.0.3

Gens fix for new production middleman

  • Updated access link from wgs folder to tumwgs for new Middleman

v2.0.2

Updated Sentieon Version

  • Uppdated the Sentieon version to 202308.03
  • Seperated QC module to calculation and collection module
  • Trannel profile was changed to more appropriate test
  • Test profile was update

v2.0.1

Gens Load Fix

  • added --case-id $group to the gens load command
  • fixed the issue with memory requirements for the big process
  • homogenized between the production and the git versions

Release date

* version 2.0.0 on September 30 2022

Features

*	DSL2 based implemetation of tumor WGS
*	Able to adabpt to both Hematology and Solid WGS questions
* 	GENS for both normal and tumor
* 	Able to handle both tumor/normal and tumor only analysis
* 	COYOTE can handle unfiltered SNV list but tagged SNV from gene panel can be selected

Fixes

* 	Sharding from 32 to 8 for better I/O specially with bqsr steps in senteion
* 	Changes with the profile configs
* 	Changes with the coyote to include sample-wgs