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| Original file line number | Diff line number | Diff line change |
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| name: bcftools_annotate | ||
| namespace: bcftools | ||
| description: | | ||
| Add or remove annotations from a VCF/BCF file. | ||
| keywords: [Annotate, VCF, BCF] | ||
| links: | ||
| homepage: https://samtools.github.io/bcftools/ | ||
| documentation: https://samtools.github.io/bcftools/bcftools.html#annotate | ||
| repository: https://github.com/samtools/bcftools | ||
| issue_tracker: https://github.com/samtools/bcftools/issues | ||
| references: | ||
| doi: https://doi.org/10.1093/gigascience/giab008 | ||
| license: MIT/Expat, GNU | ||
| requirements: | ||
| commands: [bcftools] | ||
| authors: | ||
| - __merge__: /src/_authors/theodoro_gasperin.yaml | ||
| roles: [author] | ||
|
|
||
| argument_groups: | ||
| - name: Inputs | ||
| arguments: | ||
| - name: --input | ||
| alternatives: -i | ||
| type: file | ||
| multiple: true | ||
| description: Input VCF/BCF file. | ||
| required: true | ||
|
|
||
| - name: Outputs | ||
| arguments: | ||
| - name: --output | ||
| alternatives: -o | ||
| direction: output | ||
| type: file | ||
| description: Output annotated file. | ||
| required: true | ||
|
|
||
| - name: Options | ||
| description: | | ||
| For examples on how to use use bcftools annotate see http://samtools.github.io/bcftools/howtos/annotate.html. | ||
| For more details on the options see https://samtools.github.io/bcftools/bcftools.html#annotate. | ||
| arguments: | ||
|
|
||
| - name: --annotations | ||
| alternatives: --a | ||
| type: file | ||
| description: | | ||
| VCF file or tabix-indexed FILE with annotations: CHR\tPOS[\tVALUE]+ . | ||
| - name: --columns | ||
| alternatives: --c | ||
| type: string | ||
| description: | | ||
| List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. | ||
| See man page for details. | ||
| - name: --columns_file | ||
| alternatives: --C | ||
| type: file | ||
| description: | | ||
| Read -c columns from FILE, one name per row, with optional --merge_logic TYPE: NAME[ TYPE]. | ||
| - name: --exclude | ||
| alternatives: --e | ||
| type: string | ||
| description: | | ||
| Exclude sites for which the expression is true. | ||
| See https://samtools.github.io/bcftools/bcftools.html#expressions for details. | ||
| example: 'QUAL >= 30 && DP >= 10' | ||
|
|
||
| - name: --force | ||
| type: boolean_true | ||
| description: | | ||
| continue even when parsing errors, such as undefined tags, are encountered. | ||
| Note this can be an unsafe operation and can result in corrupted BCF files. | ||
| If this option is used, make sure to sanity check the result thoroughly. | ||
| - name: --header_line | ||
| alternatives: --H | ||
| type: string | ||
| description: | | ||
| Header line which should be appended to the VCF header, can be given multiple times. | ||
| - name: --header_lines | ||
| alternatives: --h | ||
| type: file | ||
| description: | | ||
| File with header lines to append to the VCF header. | ||
| For example: | ||
| ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line"> | ||
| ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line"> | ||
| - name: --set_id | ||
| alternatives: --I | ||
| type: string | ||
| description: | | ||
| Set ID column using a `bcftools query`-like expression, see man page for details. | ||
| - name: --include | ||
| type: string | ||
| description: | | ||
| Select sites for which the expression is true. | ||
| See https://samtools.github.io/bcftools/bcftools.html#expressions for details. | ||
| example: 'QUAL >= 30 && DP >= 10' | ||
|
|
||
| - name: --keep_sites | ||
| alternatives: --k | ||
| type: boolean_true | ||
| description: | | ||
| Leave --include/--exclude sites unchanged instead of discarding them. | ||
| - name: --merge_logic | ||
| alternatives: --l | ||
| type: string | ||
| choices: | ||
| description: | | ||
| When multiple regions overlap a single record, this option defines how to treat multiple annotation values. | ||
| See man page for more details. | ||
| - name: --mark_sites | ||
| alternatives: --m | ||
| type: string | ||
| description: | | ||
| Annotate sites which are present ("+") or absent ("-") in the -a file with a new INFO/TAG flag. | ||
| - name: --min_overlap | ||
| type: string | ||
| description: | | ||
| Minimum overlap required as a fraction of the variant in the annotation -a file (ANN), | ||
| in the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF). | ||
| By default overlaps of arbitrary length are sufficient. | ||
| The option can be used only with the tab-delimited annotation -a file and with BEG and END columns present. | ||
| - name: --no_version | ||
| type: boolean_true | ||
| description: | | ||
| Do not append version and command line information to the output VCF header. | ||
| - 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: --pair_logic | ||
| type: string | ||
| choices: ['snps', 'indels', 'both', 'all', 'some', 'exact'] | ||
| description: | | ||
| Controls how to match records from the annotation file to the target VCF. | ||
| Effective only when -a is a VCF or BCF file. | ||
| The option replaces the former uninuitive --collapse. | ||
| See Common Options for more. | ||
| - name: --regions | ||
| alternatives: --r | ||
| type: string | ||
| description: | | ||
| Restrict to comma-separated list of regions. | ||
| Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…]. | ||
| example: '20:1000000-2000000' | ||
|
|
||
| - name: --regions_file | ||
| alternatives: --R | ||
| type: file | ||
| description: | | ||
| Restrict to regions listed in a file. | ||
| Regions can be specified either on a VCF, BED, or tab-delimited file (the default). | ||
| For more information check manual. | ||
| - name: --regions_overlap | ||
| type: string | ||
| choices: ['pos', 'record', 'variant', '0', '1', '2'] | ||
| description: | | ||
| This option controls how overlapping records are determined: | ||
| set to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); | ||
| set to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, | ||
| and includes indels with POS at the end of a region, which are technically outside the region); | ||
| or set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation "TA>T-" vs the true sequence variation "A>-"). | ||
| - name: --rename_annotations | ||
| type: file | ||
| description: | | ||
| Rename annotations: TYPE/old\tnew, where TYPE is one of FILTER,INFO,FORMAT. | ||
| - name: --rename_chromosomes | ||
| type: file | ||
| description: | | ||
| Rename chromosomes according to the map in file, with "old_name new_name\n" pairs | ||
| separated by whitespaces, each on a separate line. | ||
| - name: --samples | ||
| type: string | ||
| description: | | ||
| Subset of samples to annotate. | ||
| See also https://samtools.github.io/bcftools/bcftools.html#common_options. | ||
| - name: --samples_file | ||
| type: file | ||
| description: | | ||
| Subset of samples to annotate in file format. | ||
| See also https://samtools.github.io/bcftools/bcftools.html#common_options. | ||
| - name: --single_overlaps | ||
| type: boolean_true | ||
| description: | | ||
| Use this option to keep memory requirements low with very large annotation files. | ||
| Note, however, that this comes at a cost, only single overlapping intervals are considered in this mode. | ||
| This was the default mode until the commit af6f0c9 (Feb 24 2019). | ||
| - name: --remove | ||
| alternatives: --x | ||
| type: string | ||
| description: | | ||
| List of annotations to remove. | ||
| Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter. | ||
| Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT. | ||
| To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER). | ||
| "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT". | ||
| resources: | ||
| - type: bash_script | ||
| path: script.sh | ||
|
|
||
| test_resources: | ||
| - type: bash_script | ||
| path: test.sh | ||
|
|
||
| engines: | ||
| - type: docker | ||
| image: debian:stable-slim | ||
| setup: | ||
| - type: apt | ||
| packages: [bcftools, procps] | ||
| - type: docker | ||
| run: | | ||
| echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt | ||
| test_setup: | ||
| - type: apt | ||
| packages: [tabix] | ||
|
|
||
| runners: | ||
| - type: executable | ||
| - type: nextflow | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| ``` | ||
| bcftools annotate -h | ||
| ``` | ||
|
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| annotate: option requires an argument -- 'h' | ||
|
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||
| About: Annotate and edit VCF/BCF files. | ||
| Usage: bcftools annotate [options] VCF | ||
|
|
||
| Options: | ||
| -a, --annotations FILE VCF file or tabix-indexed FILE with annotations: CHR\tPOS[\tVALUE]+ | ||
| -c, --columns LIST List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details | ||
| -C, --columns-file FILE Read -c columns from FILE, one name per row, with optional --merge-logic TYPE: NAME[ TYPE] | ||
| -e, --exclude EXPR Exclude sites for which the expression is true (see man page for details) | ||
| --force Continue despite parsing error (at your own risk!) | ||
| -H, --header-line STR Header line which should be appended to the VCF header, can be given multiple times | ||
| -h, --header-lines FILE Lines which should be appended to the VCF header | ||
| -I, --set-id [+]FORMAT Set ID column using a `bcftools query`-like expression, see man page for details | ||
| -i, --include EXPR Select sites for which the expression is true (see man page for details) | ||
| -k, --keep-sites Leave -i/-e sites unchanged instead of discarding them | ||
| -l, --merge-logic TAG:TYPE Merge logic for multiple overlapping regions (see man page for details), EXPERIMENTAL | ||
| -m, --mark-sites [+-]TAG Add INFO/TAG flag to sites which are ("+") or are not ("-") listed in the -a file | ||
| --min-overlap ANN:VCF Required overlap as a fraction of variant in the -a file (ANN), the VCF (:VCF), or reciprocal (ANN:VCF) | ||
| --no-version Do not append version and command line to the header | ||
| -o, --output FILE Write output to a file [standard output] | ||
| -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v] | ||
| --pair-logic STR Matching records by <snps|indels|both|all|some|exact>, see man page for details [some] | ||
| -r, --regions REGION Restrict to comma-separated list of regions | ||
| -R, --regions-file FILE Restrict to regions listed in FILE | ||
| --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1] | ||
| --rename-annots FILE Rename annotations: TYPE/old\tnew, where TYPE is one of FILTER,INFO,FORMAT | ||
| --rename-chrs FILE Rename sequences according to the mapping: old\tnew | ||
| -s, --samples [^]LIST Comma separated list of samples to annotate (or exclude with "^" prefix) | ||
| -S, --samples-file [^]FILE File of samples to annotate (or exclude with "^" prefix) | ||
| --single-overlaps Keep memory low by avoiding complexities arising from handling multiple overlapping intervals | ||
| -x, --remove LIST List of annotations (e.g. ID,INFO/DP,FORMAT/DP,FILTER) to remove (or keep with "^" prefix). See man page for details | ||
| --threads INT Number of extra output compression threads [0] | ||
|
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| Examples: | ||
| http://samtools.github.io/bcftools/howtos/annotate.html | ||
|
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