Man pages for MRCIEU/gwasvcf
Tools for Dealing with GWAS Summary Data in VCF Format
| check_bcftools | Check if the tools_bcftools option is set |
| check_plink | Check if the tools_plink option is set |
| create_ldref_sqlite | Create LD reference sqlite database for tags |
| create_pval_index_from_vcf | Create pval index from GWAS-VCF file |
| create_rsidx_index_from_vcf | Create RSID index from VCF |
| create_rsidx_sub_index | Create new index from existing index using a subset of rsids |
| create_vcf | Create GWAS vcf |
| get_ld_proxies | Find LD proxies for a set of SNPs |
| gwasvcf_to_summaryset | Create a SummarySet |
| merge_vcf | Merge two GWAS VCF objects |
| parse_chrompos | Parse chromosome:position |
| pipe | Pipe operator |
| proxy_match | Extract SNPs from vcf file |
| query_chrompos_bcftools | Query chromosome and position using bcftools |
| query_chrompos_file | Query vcf file, extracting by chromosome and position |
| query_chrompos_vcf | Query chrompos from vcf object |
| query_gwas | Query data from vcf file |
| query_pval_bcftools | Query p-value using bcftools |
| query_pval_file | Query pval from vcf file |
| query_pvali | Query pvali |
| query_pval_sqlite3 | Query pval from file using pvali index |
| query_pval_vcf | Query based on p-value threshold from vcf |
| query_rsid_bcftools | Query |
| query_rsid_file | Query vcf file, extracting by rsid |
| query_rsid_rsidx | Query rsid from file using rsidx index |
| query_rsid_vcf | Query rsid from vcf object |
| query_rsidx | Query rsidx |
| set_bcftools | Set bcftools binary location |
| set_plink | Set plink binary location |
| sqlite_ld_proxies | Lookup LD proxies from sqlite database |
| VariantAnnotation | VariantAnnotation |
| vcflist_overlaps | Reduce list of VCFs to intersecting regions |
| vcf_to_granges | Convert vcf format to granges format |
| vcf_to_tibble | Convert vcf format to tibble (data frame) |
