VCAT v3.0 and FASTQ Toolkit v2.2 – Usability Improvements and Gold Reference Updates

The Variant Calling Assessment Tool (VCAT) v3.0 BaseSpace® App has improved usability, several new gold references, adds BED file stratification, and delivers an enhanced in-browser report.

Improved VCF file selection

  • File chooser now allows multi-selection of VCFs
  • Easier usage of alternative labels for VCF files
  • File chooser now defaults to the current Project
  • Improved VCF file tooltips now show analysis name

Gold Reference Additions and Updates

  • Added Platinum Genomes reference data for NA12877 (male spouse of NA12878)
  • Added NIST GiaB gold reference data for NA24385 (Ashkenazi male)
  • Added gold reference data and novelty rate calculations for hg38
  • Updated NIST Genome in a Bottle reference data to version 3.2.2
  • Updated Platinum Genomes reference data to version 2016-01

Improved Reporting

  • Export tables to clipboard, CSV, or Excel
  • Show/hide columns
  • Pagination control
  • Instant row filtering

BED file stratification

Tool Updates

  • Updated Haplotype Compare from 0.2.6 to 0.2.9
  • Changed from VCFtools to BCFtools for VCF stats and intersect generation
  • Changed to BEDtools for BED file processing
  • Changed to multi-node processing of input VCFs to improve speed






The FASTQ Toolkit v2.2 App update adds new trimming and paired-end singleton filtering features.

  • Fixed issue with adapter trimming using the default adapter drop down option
  • Added 5′-end and 3′-end quality trimming options
  • Added sliding window quality trimming feature
  • Added filter for singleton reads in paired-end data
  • Use sample ID for app session name instead of analysis name



We hope you find VCAT 3.0 and FASTQ Toolkit 2.2 useful. Questions can be directed to

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.