Multiple functionalities are implemented in TrioGen, each coming with its own command line.
- LinearModel: Runs {child, mother, father} trio linear models genome-wide or one specific regions of the genome.
- Extract: Extracts results for specific phenotypes or variants from the LinearModel command line.
- LdMatrix: Computes an LD matrix from unrelated samples in trio data.
- LdPruning: Performs LD pruning on association results.
- LdValue: Returns the variants in LD with a given list of variants.
- LocusZoom: Extracts the data necessary to plot locus zoom plots.
- MendelianCheck: Writes a report on mendelian errors in a given data set.
- PRS: Computes trio polygenic risk scores.
- SimpleScore: Computes simple risk scores based on a list of weights.
- VariantData: Exports a matrix of standardized trio genotypes and phenotypes for a set of variants.
- VariantFile: Builds a variant file from a list of variant ids.
- VcfToBgen: Exports the phased genotypes of trios from a vcf to a phased v1.3 bgen file.