Trio_matrix(dataset, pedigree)īuilds and returns a matrix where columns correspond to trios and entries contain genotypes for the trio.Ĭompute common variant statistics (quality control metrics). Performs the transmission disequilibrium test on trios. Transmission_disequilibrium_test(dataset, …)
Summarize the variants present in a dataset and print the results. Split multiallelic variants for datasets that contain one or more fields from a standard high-throughput sequencing entry schema. Test each keyed group of rows for association by linear or logistic SKAT test.Ĭompute genomic inflation factor (lambda GC) from an Expression of p-values. Skat(key_expr, weight_expr, y, x, covariates) The logistic sequence kernel association test (SKAT). _logistic_skat(group, weight, y, x, covariates) Nirvana(dataset, config)Ĭompute per-sample metrics useful for quality control. Returns a maximal subset of variants that are nearly uncorrelated within each window.įind Mendel errors count per variant, individual and nuclear family.ĭe_novo(mt, pedigree, pop_frequency_prior, *)Ĭall putative de novo events from trio data. Ld_matrix(entry_expr, locus_expr, radius)Ĭomputes the windowed correlation (linkage disequilibrium) matrix between variants. Impute sex of samples by calculating inbreeding coefficient on the X chromosome. Run principal component analysis (PCA) on the Hardy-Weinberg-normalized genotype call matrix.Ĭompute the genetic relatedness matrix (GRM).Ĭomputes the realized relationship matrix (RRM).
#Skat definition update
Generate a matrix table of variants, samples, and genotypes using the Balding-Nichols or Pritchard-Stephens-Donnelly model.Ĭalculate call concordance with another dataset.įilter alternate alleles and update standard GATK entry fields. The Hail-maintained VEP configuration for GRCh38 for VEP version 95.īalding_nichols_model(n_populations, …) VEPConfigGRCh38Version95(*, data_bucket, …) The Hail-maintained VEP configuration for GRCh37 for VEP version 85. VEPConfigGRCh37Version85(*, data_bucket, …)
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