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
- User can load an arbitrary number of custom BED files to use in their analysis
- Stratify results across entire genome/panel and separately for each BED file selected
- BED files can be loaded into BaseSpace Projects via BaseSpace Copy or BaseMount
- Some example BED files to use with this feature can be found here:
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 basespacelabs@illumina.com.