Release note June

Johanna Samuelsson
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Release note June

Written by Johanna Samuelsson in

Recently published apps and resources

This release introduced a new set of tool upgrades to the Public Apps Gallery on the Seven Bridges Platform, including VCFtools, GATK, and Regenie for variant processing, variant calling, and large-scale genetic association studies.

VCFtools Suite for Variant Processing and Comparison

A comprehensive collection of VCFtools-based applications has been upgraded to support routine variant-processing and quality-control workflows. These tools improve interoperability across genomic analysis pipelines while streamlining common data manipulation tasks.

The upgraded applications enable users to:

  • Filter variants using quality, genotype, region, and variant-level criteria with VCFtools Filter.
  • Separate SNPs and indels using VCFtools Keep SNPs and VCFtools Keep Indels.
  • Merge, concatenate, sort, and subset variant datasets using VCFtools Merge, Concat, Sort, and Subset.
  • Perform variant intersection analyses with VCFtools Isec, Venn2, and Venn3.
  • Assess Hardy-Weinberg Equilibrium using VCFtools Hardy and VCFtools Hwe.
  • Convert between VCF versions using VCFtools Convert to support downstream tool compatibility.

These enhancements simplify routine variant curation and analysis workflows for genomic researchers.

GATK Best-Practice Components

Several key Genome Analysis Toolkit (GATK) applications have been upgraded, enabling users to build variant-calling workflows aligned with widely adopted best-practice methodologies.

The upgraded applications include:

  • BaseRecalibrator
  • ApplyBQSR
  • GatherBQSRReports
  • HaplotypeCaller
  • VariantFiltration
  • GenomicsDBImport

Together, these tools support base-quality score recalibration, germline variant discovery, joint genotyping workflows, and downstream variant filtering to improve sequencing analysis quality and consistency.

Regenie

The Public Apps Gallery has also been upgraded with Regenie, a widely used tool for whole-genome regression and large-scale genetic association studies. Regenie is designed for efficient analysis of large cohorts and supports genome-wide association testing across quantitative and binary traits, making it a valuable addition for population-scale genomics and genetic epidemiology research.

Resources

If you have questions or need help  with any of these new resources, please contact your Velsera Seven Bridges representative or email support@velsera.com. 

Johanna Samuelsson