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Release notes - November 13, 2023

6 months ago by Marko Marinkovic

Improved error messages for volume imports

To provide you with more detailed information about each import from an attached volume and enable you to resolve import issues independently, we have added improved notifications in the recently implemented Activity center, available by clicking Open activity center in the Activity feed. When any of the items from a particular import fails, you will be able to see an error message and a corresponding error code for each of the items, allowing you to understand and try to fix the issue. Furthermore, a description and link to the relevant documentation will be provided for each import from a volume.

Recently published apps

The Change-O 1.3.0 toolkit is the latest new toolkit addition in our Public Apps gallery. It includes the following apps: 

  • DefineClones - assigns Ig sequences into clonal groups. 
  • BuildTrees - creates IgPhyML input files. 
  • ParseDb - parses and updates input database files. 
  • AlignRecords - multiple aligns sequence fields. 
  • AssignGenes - assigns V(D)J gene annotations. 
  • MakeDb - creates standardized databases output from the input germline alignment results. 
  • CreateGermlines - reconstructs germline V(D)J sequences for alignment data. 
  • ConvertDb - parses input tab-delimited database files and converts them to different output formats. 

Recently updated apps

We updated Broad Institute’s best practices for somatic copy number variant discovery analyses, to version 4.2.5.0 in our Public Apps gallery: 

GATK Somatic CNV Panel Workflow 4.2.5.0 - used for creating a panel of normals (PON) given a set of normal samples. 

GATK Somatic CNV Pair Workflow 4.2.5.0 - used for detecting copy number variants (CNVs) from WES/WGS single sample data in tumor-only or matched-normal mode.