SVS 8.3.4 Release Notes
- Replaced current VCF importer with a new Import Wizard, Import > Import VCFs. This importer is optimized to bring in data faster as well as merge files with advanced options that were introduced in VarSeq.
- Add allele information to the marker map after recoding genotypes to either DD/Dd/ddor numeric format.
- If recoding based on Reference allele, adds the Alternates allele field if not present.
- If recoding based on Major/Minor allele count, adds a Major Allele and Minor Allele field to the marker map.
- Bayesian Genomic Prediction:
- Added chain parameters to the options dialog including Number of Iterations, Burn-in, and Thinning.
- Added option to set the initial value of pi.
- Output a trace spreadsheet containing the sampled values for pi, variances, and number of markers included in the iteration.
- Output numeric plots of the values in the trace spreadsheet.
- K-Fold Cross Validation (K-Fold Cross Validation):
- Recode genotypes to numeric model first to ensure consistency between folds, dropping multi-allelic markers.
- Added observed phenotype to estimates by sample output.
- Added fold predicted in to final results spreadsheet.
- Now able to run K-Fold with multiple iterations, this allows for compiling iteration statistics. See Statistics for more information.
- Added Genotype > Predict Phenotypes from Existing Results script. This script takes the output of K-Fold Cross-Validation and applies the model to a new genotype spreadsheet (with or without covariates) see Predict Phenotypes From Existing Results for more information.
- Plot > Autocorrelation Plots now available, this can be used in conjunction with the trace output from Bayesian Genomic Prediction or on other data.
- Fixed numeric representation for operating systems with the region set to a location that uses different thousands or decimal separators. Now always uses ”,” as the thousands separator and ”.” as the decimal separator.
- Fixed index assignment operator for arrays so Expression Editor can use specific entries to calculate new fields.
- Genomic prediction methods GBLUP, Bayesian, and K-Fold bug fixes:
- Check for covariance
- Handle duplicate row labels by using the row label and index for matching.
- Fixed importing of INFO files in the Import Impute2 GWAS Files scripts so that it now accepts one info file per genotype file.
- Fixed spreadsheets Scripts menu on MacOS X so that scripts saved in this menu can be selected. Also the menu will now stay visible when no scripts are available.
- Fixed setting image size for Save as Image from Plot Viewer (non-genomic) plots. This bug was introduced in version 8.3.2.
- Fixed Compare Variants Across Several Spreadsheets tool so it now works correctly for spreadsheets that have no marker map.
- Prevented crash when renaming marker mapped labels to Chromosome:Position when there is a marker-mapped dependent column.
- On MacOS X prevented hangs after:
- Joining and merging spreadsheets
- Creating top-level spreadsheets
- Fixed error with Calculate Alt Read Ratio script when additional phenotype columns are present.
- Prevented failure to create marker map from spreadsheet when there is a “slash” in the marker map name.
- Added additional output to Fisher’s Exact Test for Binary Predictors including direction of effect, per marker sample totals, and odd ratio confidence intervals.
- Updated default RefSeq gene annotation source based on GRCh37_g1k build to include Locus Reference Genome (LRG) identifiers, updated source name is RefSeq Genes 105v2, NCBI.
- Modified warning message for Recode Genotypes to be more informative when using the Reference vs Alternate option and fewer than half the mapped markers have a genotype with a reference allele. Also, the recode dialog is now disabled while processing.