diff --git a/src/bcftools/bcftools_concat/config.vsh.yaml b/src/bcftools/bcftools_concat/config.vsh.yaml index 7f5f5f35..2688e373 100644 --- a/src/bcftools/bcftools_concat/config.vsh.yaml +++ b/src/bcftools/bcftools_concat/config.vsh.yaml @@ -39,125 +39,101 @@ argument_groups: - name: Options arguments: - # - name: --atomize - # alternatives: -a - # type: boolean_true - # description: | - # Decompose complex variants (e.g., MNVs become consecutive SNVs). - - # - name: --atom_overlaps - # type: string - # choices: [".", "*"] - # description: | - # Use the star allele (*) for overlapping alleles or set to missing (.). - - # - name: --check_ref - # alternatives: -c - # type: string - # choices: ['e', 'w', 'x', 's'] - # description: | - # Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites. - - # - name: --remove_duplicates - # alternatives: -d - # type: string - # choices: ['snps', 'indels', 'both', 'all', 'exact', 'none'] - # description: Remove duplicate snps, indels, both, all, exact matches, or none (old -D option). - - # - name: --fasta_ref - # alternatives: -f - # type: file - # description: Reference fasta sequence file. - - # - name: --force - # type: boolean_true - # description: | - # Try to proceed even if malformed tags are encountered. - # Experimental, use at your own risk. - - # - name: --keep_sum - # type: string - # description: | - # Keep vector sum constant when splitting multiallelics (see github issue #360). - - # - name: --multiallelics - # alternatives: -m - # type: string - # choices: ['+snps', '+indels', '+both', '+any', '-snps', '-indels', '-both', '-any'] - # description: | - # Split multiallelics (-) or join biallelics (+), type: snps, indels, both, any [default: both]. - - # - name: --no_version - # type: boolean_true - # description: Do not append version and command line information to the header. - - # - name: --do_not_normalize - # alternatives: -N - # type: boolean_true - # description: Do not normalize indels (with -m or -c s). + - name: --allow_overlaps + alternatives: -a + type: boolean_true + description: | + First coordinate of the next file can precede last record of the current file. - # - name: --output_type - # alternatives: --O - # type: string - # choices: ['u', 'z', 'b', 'v'] - # description: | - # Output type: - # u: uncompressed BCF - # z: compressed VCF - # b: compressed BCF - # v: uncompressed VCF + - name: --compact_PS + alternatives: -c + type: boolean_true + description: | + Do not output PS tag at each site, only at the start of a new phase set block. - # - name: --old_rec_tag - # type: string - # description: Annotate modified records with INFO/STR indicating the original variant. - - # - name: --regions - # alternatives: -r - # type: string - # description: Restrict to comma-separated list of regions. - - # - name: --regions_file - # alternatives: -R - # type: file - # description: Restrict to regions listed in a file. - - # - name: --regions_overlap - # type: string - # choices: ['pos', 'record', 'variant', '0', '1', '2'] - # description: | - # Include if POS in the region (0), record overlaps (1), variant overlaps (2). - - # - name: --site_win - # alternatives: -w - # type: integer - # description: | - # Buffer for sorting lines that changed position during realignment. - - # - name: --strict_filter - # alternatives: -s - # type: boolean_true - # description: When merging (-m+), merged site is PASS only if all sites being merged PASS. - - # - name: --targets - # alternatives: -t - # type: string - # description: Similar to -r but streams rather than index-jumps. - - # - name: --targets_file - # alternatives: -T - # type: file - # description: Similar to -R but streams rather than index-jumps. - - # - name: --targets_overlap - # type: string - # choices: ['pos', 'record', 'variant', '0', '1', '2'] - # description: | - # Include if POS in the region (0), record overlaps (1), variant overlaps (2). - - # - name: --threads - # type: integer - # description: | - # Use multithreading with the specified number of worker threads. + - name: --remove_duplicates + alternatives: -d + type: string + choices: ['snps', 'indels', 'both', 'all', 'exact'] + description: | + Output duplicate records present in multiple files only once: . + + - name: --file_list + alternatives: -f + type: file + description: Read the list of files from a file. + + - name: --ligate + alternatives: -l + type: boolean_true + description: Ligate phased VCFs by matching phase at overlapping haplotypes. + + - name: --ligate_force + type: boolean_true + description: Ligate even non-overlapping chunks, keep all sites. + + - name: --ligate_warn + type: boolean_true + description: Drop sites in imperfect overlaps. + + - name: --no_version + type: boolean_true + description: Do not append version and command line information to the header. + + - name: --naive + alternatives: -n + type: boolean_true + description: Concatenate files without recompression, a header check compatibility is performed. + + - name: --naive_force + type: boolean_true + description: | + Same as --naive, but header compatibility is not checked. + Dangerous, use with caution. + + - name: --output_type + alternatives: --O + type: string + choices: ['u', 'z', 'b', 'v'] + description: | + Output type: + u: uncompressed BCF + z: compressed VCF + b: compressed BCF + v: uncompressed VCF + + - name: --min_PQ + alternatives: -q + type: integer + description: Break phase set if phasing quality is lower than . + examples: 30 + + - name: --regions + alternatives: -r + type: string + description: Restrict to comma-separated list of regions. + + - name: --regions_file + alternatives: -R + type: file + description: Restrict to regions listed in a file. + + - name: --regions_overlap + type: string + choices: ['pos', 'record', 'variant', '0', '1', '2'] + description: | + Include if POS in the region (0), record overlaps (1), variant overlaps (2). + + - name: --threads + type: integer + description: | + Use multithreading with the specified number of worker threads. + + - name: --verbose + alternatives: -v + type: integer + choices: [0, 1] + description: Set verbosity level. resources: - type: bash_script