CI
db2f4203b8
Build pipeline: viash-hub.biobox.main-n2mwd
Source commit: c3ba4a7849
Source message: Bcftools annotate (#143)
* Initial commit
* Update config.vsh.yaml
* changes in config file
* Update script.sh
* Help File
* Update script.sh
* Update test.sh
* bug fixing and adding tests
* Update test.sh
* Update test.sh
* adding 3rd test
* More tests
* Moreee tests
* Update test.sh
* small changes
* Update CHANGELOG.md
* Update config.vsh.yaml
* bug fixing on config
* Requested changes
---------
Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com>
42 lines
3.0 KiB
Plaintext
42 lines
3.0 KiB
Plaintext
```
|
|
bcftools annotate -h
|
|
```
|
|
|
|
annotate: option requires an argument -- 'h'
|
|
|
|
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]
|
|
|
|
Examples:
|
|
http://samtools.github.io/bcftools/howtos/annotate.html
|
|
|