SVS 8.3.0 Release Notes
- SKAT-O: Added SKAT-O as a collapsing method for large-N DNA Sequencing analysis. It can be found in the DNA-Seq > Collapsing Methods menu. See Optimized Sequence Kernel Association Test (SKAT-O).
- Bayes-Cπ: Bayesian methods to compute additive genetic merits by sample and allele substitution effects (ASE) by marker. See Bayes C and C-pi Genomic Prediction Analysis.
- The variance and standard error estimates of pseudo-heritability are now being computed for EMMAX and GBLUP and printed in the node change log. See Estimating the Variance of Heritability.
- Fixed the variance component estimates for GBLUP and MLMM. These estimates were systematically inflated. The only results affected were the variance component estimates themselves. All other results were unaffected.
- Import Impute2 no longer gives errors if:
- A chromosome number is not in the name of the genotype file
- Only dosages are imported and genotypes are not converted.
- Saving data in the VCF format now handles real (float) valued fields correctly. Also fixed printing of missing value fields in the INFO field.
- Exporting data in the VCF format from the data source library now:
- Correctly places the RS ID in the identifier field instead of creating a new INFO field.
- Removes white space from symbol names and replaces with underscores
- Allele classification choice is now remembered for various genotype functions that have a allele frequency vs ref/alt allele choice including Genotype Statistics by Marker, Genotype Filtering by Marker, Genotype Principal Component Analysis, Genotype Association Tests.
- Annotate and Filter Variants bugs fixed:
- Allow filtering with variant tracks if the series name for the annotation source is empty.
- Do not fail on variant sources that do not have a build with a valid dbNSFP source.
- Present informative error when a reference allele field is missing in the spreadsheet’s marker map instead of presenting an uninformative python error.
- Updated Score Compound Heterozygous Regions to handle spreadsheets that contain data from both chromosomes and scaffolds. Now, skips all segments that are not also present in the gene annotation source while correctly analyzing those that are present.
- Bug fixed in Mendelian Error Check. If the “Report Mendelian Inconsistencies” option was selected, it resulted in the “Mendelian Errors by Marker” output being off by six marker rows. If the “Remove Mendelian Inconsistencies” option was selected, it resulted in the “Removed Mendelian Inconsistencies” output being off by six marker columns.
- Fixed bug in Variant Classification where filtering was selected but the corresponding spreadsheet was not selected for output.
- Prevented Fixation Index Fst from crashing when a categorical dependent column was selected with more than 20 categories.
- Nonlinear Regression of R Squared on Distance no longer errors out when there are no missing values.
- Fixed column move functions in the spreadsheet editor to only move the selected column and not the selected column and an adjacent column. This affects Move Column > Move Column to the Front and Move Column > Move Column to the Far Right.
- Converting NCBI GFF files to an annotation source using Convert NCBI GFF Files to Annotation Track will use the assembly file to rename the “NC_” segment names to the chromosome names used in GenomeBrowse for plotting the annotation sources.
- Notes and tags for Regression Viewers are now being correctly saved and reloaded on close and reopen of projects.
- Added option to include a note when saving an edited spreadsheet that will be included in the node change log for the spreadsheet. The node log now also indicates that the spreadsheet was created by editing a spreadsheet and contains the name of the original spreadsheet.
- Genotype Statistics per Sample now uses the assembly file for the project species and build to identify allosomes for Gender Chromosome Statistics.
- Added total number of runs per sample to Numeric > CNAM Output > Count Number of Segments Per Sample.
- Removed preview boxes for the Expression Editor when adding a Filter by Sample in GenomeBrowse for Variant Maps and Heat Maps.