Man pages for RajLabMSSM/echotabix
echoverse module: automated creation and querying of tabix files
| check_delimiter | Check delimiter |
| construct_outputs | Construct outputs |
| construct_query | Construct query |
| construct_subset_vcf_name | Construct the path to vcf subset |
| construct_tabix_path | Construct tabix path |
| construct_vcf_path | VCF path |
| convert | Convert to tabix |
| convert_and_query | Convert and query |
| DF_to_dt | DataFrame to data.table |
| dt_to_vcf | data.table to VCF |
| fill_NA | Fill NAs in an LD matrix |
| filter_vcf_query_samples | Filter VCF query samples |
| get_chain_file | Download chain file for liftover |
| get_locus_vcf_folder | Get VCF storage folder |
| granges_to_dt | GenomicRanges to data.table |
| granges_to_string | GRanges to string |
| index | Tabix-index a file |
| index_conda | Tabix-index a file: conda |
| index_rsamtools | Tabix-index a file: Rsamtools |
| index_seqminer | Tabix-index a file: 'seqminer' |
| index_variantannotation | Tabix-index file: VariantAnnotation |
| infer_chrom_type | Infer chromosome type |
| is_tabix | Is tabix |
| is_vcf | Is VCF |
| liftover | Genome build liftover |
| query | Query tabix |
| query_table | Query a tabix file |
| query_table_conda | Query tabular: conda |
| query_table_genomicfiles | Query tabular: 'GenomicFiles' |
| query_table_rsamtools | Query tabular: 'Rsamtools' |
| query_table_seqminer | Query tabular: 'seqminer' |
| query_vcf | Query VCF file |
| query_vcf_conda | Query VCF: 'conda' |
| query_vcf_rtracklayer | Query VCF: 'rtracklayer' |
| query_vcf_seqminer | Query VCF: 'seqminer' |
| query_vcf_variantannotation | Query VCF: 'VariantAnnotation' |
| read_bgz | Read bgz |
| report_time | Report time at end of function |
| rhtslib_warning | 'Rsamtools' warning |
| rm_tbi | Remove tbi |
| run_bgzip | Run bgzip |
| run_bgzip_conda | Run bgzip: conda |
| run_bgzip_rsamtools | Run bgzip: Rsamtools |
| run_gunzip | Run gunzip |
| run_gunzip_conda | Run gunzip: conda |
| run_gunzip_rutils | Run gunzip: R.utils |
| save_vcf | Save VCF |
| scanTabix_to_dt | scanTabix to data.table |
| select_method | Select method |
| sort_coordinates | Sort coordinates |
| sort_coordinates_bash | Sort coordinates: bash |
| sort_coordinates_datatable | Sort coordinates: data.table |
| suffixes | List supported file formats |
| vcf_to_dt | Variant Call Format (VCF) -> data.table |
