Man pages for imbs-hl/imbs
Collection of functions used at the IMBS
| annovar_annotate_region | Annotate variant regions |
| annovar_plink_conversion | Convert PLINK bim file to ANNOVAR input |
| change_csv_locale | Changes delimiters in csv files |
| check_command | Check if command exists |
| compare_sets | Compare two vectors with simple set theory |
| do_multirow | Combine rows with the same content |
| dot-plink_fst | Internal Fst computation with PLINK |
| dot-plink_pca | Internal PCA computation with PLINK |
| ex2pdf | Generation of Exercise Sheets and Exams in PDF Format |
| harmonize_genotypes | Genotype harmonization |
| imbs | imbs. |
| load_or_create_registry | Load or create a 'batchtools' registry |
| manhattan_plot | Create a manhattan plot |
| migrate_installed_packages | Migrate installed packages |
| named_file_path | Named file path |
| named_paste | Named paste |
| plink_dedup | Remove duplicated variants |
| plink_fst | Fst with PLINK |
| plink_ld_pruning | LD pruning with PLINK |
| plink_logistic | GWA (single variant logistic regression) with PLINK |
| plink_marker_qc | Quality control on marker level with PLINK |
| plink_merge | Merge two PLINK datasets |
| plink_merge_list | Merge multiple PLINK datasets |
| plink_normalize_vcf_conversion | Normalize and convert VCF files to PLINK binary files |
| plink_pca | PCA with PLINK |
| plink_rm_high_ld | Remove regions of high LD |
| plink_rm_long_indels | Remove very long INDELS |
| plink_sample_qc | Quality control on sample level with PLINK |
| plink_sex_imputation | Sex imputation with PLINK |
| plink_subset | Subset samples and variants using PLINK |
| plink_vcf_conversion | Convert VCF files to PLINK binary files |
| plink_write_ids | Write SNP or sample IDs to file |
| print_3ptable | print_3ptable |
| qw | Emulate Perl's 'qw' (quoted words) function |
| read_sample | Read SNPTEST sample file |
| system_call | Wrapper for 'system2' |
| update_system2_job | update_system2_job |
| vcf_normalization | Normalize VCF file to bi-allelic variants |
| verbatimize | Verbatimize string |
