Command line tools

GAIn installs the command line tools below. Each tool prints its options with --help.

GRR management

grr_browse: list the resources of the configured GRRs.
grr_manage: build and repair the index and manifest files of a GRR.
grr_cache_repo: download the resources that an annotation pipeline uses into the GRR cache.

Annotation

annotate_tabular: annotate the variants or regions of a tabular file.
annotate_vcf: annotate the variants of a VCF file.
prepare_tabular: sort and tabix-index a tabular file, so that annotate_tabular can annotate it in parallel.
annotate_doc: write the documentation of an annotation pipeline.

Effect annotation

annotate_variant_effects: annotate the effects of the variants of a tabular file on genes.
annotate_variant_effects_vcf: annotate the effects of the variants of a VCF file on genes.
install_vep_cache: download and unpack a VEP cache for the VEP annotator plugin.

Binning

binning_tool: bin genomic scores into a fixed genome grid.
Printing a binning file with binning_tool_view: print the tables of a binning_tool file as tab-separated text.

Resource utilities

draw_score_histograms: draw the histograms of the scores of a resource.
to_gpf_gene_models_format: convert gene models to the GPF format.