Tools tl

tl.get_snp_df(variant_codes[, server])	Retrieve SNP (Single Nucleotide Polymorphism) information and overlap with genes from Ensembl.
tl.run_favor([config_file, database_dir, ...])	Annotates variants using the FAVOR database from within Python
tl.run_snpeff([command, genome_assembly, ...])	Annotates variants using the SnpEff command-line tool.
tl.run_vep([config_file, input_vcf, output, ...])	Calls the VEP command line tool from within python
tl.add_vep_annos_to_gdata(vep_anno_file, gdata)	Add VEP annotations to a gdata object.
tl.combine_annotations(gdata[, keys, ...])	Combine multiple annotation datasets into a single unified dataset.
tl.aggregate_annotations_for_varm(gdata, ...)	Aggregates a DataFrame containing variant annotations based on the specified aggregation type such that there is only row per variant id.
tl.run_burden_test(G, Y, F, gene, ...[, ...])	Perform a burden test for genetic association analysis.
tl.run_skat_test(G, Y, F, gene)
tl.beta_weighting(values[, beta_weights])	Apply beta weighting to a set of values using the Beta probability density function.
tl.subset_genomic_region(gdata, chrom, ...)	Subset the gdata object to only include variants within the specified genomic region.
tl.subset_gene(gdata, gene_id[, gene_snp_map])	Subset the gdata object to only include variants that are annotated to a specific gene.