March 2024
Ability to genotype and produce related reports for human and non-human arrays in the cloud.
Configureable interfaces in Basespace that allows for flexibility and easy kick off.
Some multi-nucleotide variant (MNV) designs reverse compliment the "Allele1/2 Top" fields in the Final Report
Genotyping only works on diploid organisms at this time. Polyploid genotyping is not currently supported.
Adjustable thresholds to determine pass/fail status
Data summary plots for a quick visual check of each analysis batch
Determining detection p-value, beta-values, and m-values from each methylation sample
Deployment on BaseSpace™ Sequence Hub user interface for easy analysis kickoff
Adjustable thresholds for 21 built in controls, p-value detection, proportion probes passing, and offset correction within BaseSpace Sequence Hub to customize for user’s study needs
Thresholds are used to assign pass (1) or fail (0) status to each sample
Failed metrics can be highlighted for easy viewing
Pinpoint areas of failure including bisulfite conversion, staining, hybridization, etc. to identify assay steps in need of troubleshooting
Quantitative values for each control removing ambiguity with manual interpretation
Data summary plots with information on passing p-value detection and principal component analysis of beta values
Provides detection p-value, beta-values and m-values for each CG site per sample to use in downstream analysis
Standard thresholds may not be applicable for all discontinued, semi-custom or custom BeadChips and IDATs originating from NextSeq550
Built-in controls may not be available on all discontinued, semi-custom or custom BeadChips
December 2023
Improved star allele calling accuracy for Global Diversity Array with enhanced PGx (GDA-ePGx) BeadChips.
Reports star allele calls with quality scores for greater transparency and confidence.
Provides missing variant reporting to improve data quality.
Star Allele Calling
Star allele calling for genes listed in
For in-silico datasets, call rate ≥99%, diplotyping accuracy ≥ 90%
Corrupt or invalid GTC files will abort with an error instead of skipping. The corrupt or invalid GTC files will need to be removed before proceeding.
In the gtc-to-vcf subcommand a mismatch between BPM and CSV manifests will not cause the command to abort with an error. The mismatch will need to be addressed before proceeding.
For gtc-to-vcf, multi-allelic variants designed with multiple assays might not always collapse into one variant correctly and be reported as two separate variants instead. Some indel variants are missing from SNV VCF due to mapping issue between the designed indels and the reference genome.
PGx CNV calling and star allele calling and annotation were only validated and intended to be used with GDA_PGx_E2 product files.
Using subcommands “unsquash-duplicates” and “filter loci” during gtc-to-vcf conversion should not be used when star allele calling is desired.
Only CPIC guidelines are available for star allele annotation (metabolizer status calling) for the cloud offering. For local, CPIC and DPWG are available.
Includes reporting of the hybrid star alleles and allelic specific copy number
Provides quality score that estimates confidence in the star allele call as an additional quality metric
Star allele call rate increased through more robust error tolerance and missing data tolerance
Supporting variants and missing variants are listed and can be further reviewed
Quality score indicates confidence in result considering the missing data
Reports alternative ranked PGx star allele solutions
Allows an alternative to be investigated which may be desirable for samples with low confidence calls
Provides quality score (negative log likelihood) for alternative solutions
Function annotations for PGx genes listed in section PGx Allele Definitions and PGx Guidelines
Metabolizer and function annotations are supported for two sets of guidelines from CPIC and DPWG respectively
Activity scores are provided for CYP2C9, CYP2D6, and DPYD
CNV VCF
CNV coverage for genes listed in PGx CNVs Coverage
Compressed and indexed files for size reduction and faster reading
Updated VCF header description to indicate copy number of 5 may be reported by the software
Revised filter field delimiter to comply with VCF 4.3 specification which allows VCF parsing software to parse the file successfully
Genotyping VCF
Compressed and indexed files for size reduction and faster reading
Manifest names greater than 80 characters will cause failure when converting IDATs to GTCs.
Symbolic links for VCFs are not supported as the inputs to the “star-allele call” subcommand.
The local Linux CLI and Cloud offering do not sort the star_alleles.csv and various fields in the metabolizer_status.json. The local Windows CLI does.