- Enhancements where made to the GBLUP analysis using some of the techniques of GCTA. Most significantly of these is the ability to correct for Gene by Environment interactions. Also, the kinship matrices computed by GBLUP can be broken out by gender when using the AI REML method. See Genomic Best Linear Unbiased Predictors Analysis for more details.
- New in the spreadsheet Genotype menu is Genetic Correlation of Two Traits using GBLUP. This performs a bivariate REML analysis on two selected traits to estimate the genetic variance of each trait and the genetic covariance between two traits that can be captured by all SNPs.
- We have added LD Score Regression to the the Genotype to determine whether inflated Lambda factor statistics from your genotype association test are due to underlying population structure in your data or rather a polygenic architecture to your trait.
- When annotating a variant spreadsheet with a transcripts (a gene annotation source), you can now request that the amino acid notation use single letter notation instead of three letter notation.
- The Import Third Party Formats wizard will now import the SAS Data File files that are created when using the Save as Third Party Format exporter.
- The new Create Labels from Marker Map Field from the Spreadsheet > Edit Menu makes it easy to change your labels to RSIDs that are in your marker map.
- When importing VCF files, rows that had a ALT field of <CNV> and END value defined were being interpreted as GVCF span fields instead of being ignored on import.
- Public data sets with a “+” in their name were not downloading from the Download > Public Data menu.