SVS 8.3.4 Release Notes

New Features

  • 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.

Bugs Fixed

  • 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.

Polishes

  • 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.


Feedburner  Subscribe in a reader or via email

« Back to Support Bulletin List