bcftools/bcftools_annotate

Annotate

VCF

BCF

Description

Add or remove annotations from a VCF/BCF file.

Type

bash_script

License

MIT/Expat, GNU

Keywords

Annotate

VCF

BCF

Links

Repository

Issues

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.0 \  
  -main-script target/nextflow/bcftools/bcftools_annotate/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required multiple	Input VCF/BCF file.

Name

Type & Properties

--input

-i

file

required

multiple

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output annotated file.

Name

Type & Properties

--output

-o

file

required

output

Options

Name	Type & Properties	Description
--annotations --a	file	VCF file or tabix-indexed FILE with annotations: CHR\tPOS[\tVALUE]+ .
--columns --c	string	List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details.
--columns_file --C	file	Read -c columns from FILE, one name per row, with optional --merge_logic TYPE: NAME[ TYPE].
--exclude --e	string	Exclude sites for which the expression is true. See https://samtools.github.io/bcftools/bcftools.html#expressions for details.
--force	boolean_true	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.
--header_line --H	string	Header line which should be appended to the VCF header, can be given multiple times.
--header_lines --h	file	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">
--set_id --I	string	Set ID column using a `bcftools query`-like expression, see man page for details.
--include	string	Select sites for which the expression is true. See https://samtools.github.io/bcftools/bcftools.html#expressions for details.
--keep_sites --k	boolean_true	Leave --include/--exclude sites unchanged instead of discarding them.
--merge_logic --l	string	When multiple regions overlap a single record, this option defines how to treat multiple annotation values. See man page for more details.
--mark_sites --m	string	Annotate sites which are present ("+") or absent ("-") in the -a file with a new INFO/TAG flag.
--min_overlap	string	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.
--no_version	boolean_true	Do not append version and command line information to the output VCF header.
--output_type --O	string	Output type: u: uncompressed BCF z: compressed VCF b: compressed BCF v: uncompressed VCF
--pair_logic	string	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.
--regions --r	string	Restrict to comma-separated list of regions. Following formats are supported: chr\|chr:pos\|chr:beg-end\|chr:beg-[,…].
--regions_file --R	file	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.
--regions_overlap	string	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>-").
--rename_annotations	file	Rename annotations: TYPE/old\tnew, where TYPE is one of FILTER,INFO,FORMAT.
--rename_chromosomes	file	Rename chromosomes according to the map in file, with "old_name new_name\n" pairs separated by whitespaces, each on a separate line.
--samples	string	Subset of samples to annotate. See also https://samtools.github.io/bcftools/bcftools.html#common_options.
--samples_file	file	Subset of samples to annotate in file format. See also https://samtools.github.io/bcftools/bcftools.html#common_options.
--single_overlaps	boolean_true	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).
--remove --x	string	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".
--verbosity -v	integer	Verbosity level.

Name

Type & Properties

--annotations

--a

file

--columns

--c

string

--columns_file

--C

file

--exclude

--e

string

--force

boolean_true

--header_line

--H

string

--header_lines

--h

file

--set_id

--I

string

--include

string

--keep_sites

--k

boolean_true

--merge_logic

--l

string

--mark_sites

--m

string

--min_overlap

string

--no_version

boolean_true

--output_type

--O

string

--pair_logic

string

--regions

--r

string

--regions_file

--R

file

--regions_overlap

string

--rename_annotations

file

--rename_chromosomes

file

--samples

string

--samples_file

file

--single_overlaps

boolean_true

--remove

--x

string

--verbosity

-v

integer