bcftools/bcftools_norm

Normalize

VCF

BCF

Description

Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows;
recover multiallelics from multiple rows.

Type

bash_script

License

MIT/Expat, GNU

Keywords

Normalize

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 v0.3.0 \  
  -main-script target/nextflow/bcftools/bcftools_norm/main.nf \  
  -params-file params.yaml

Inputs

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

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output normalized VCF/BCF file.

Name

Type & Properties

--output

-o

file

required

output

Options

Name	Type & Properties	Description
--atomize -a	boolean_true	Decompose complex variants (e.g., MNVs become consecutive SNVs).
--atom_overlaps	string	Use the star allele (*) for overlapping alleles or set to missing (.).
--check_ref -c	string	Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites.
--remove_duplicates -d	string	Remove duplicate snps, indels, both, all, exact matches, or none (old -D option).
--fasta_ref -f	file	Reference fasta sequence file.
--force	boolean_true	Try to proceed even if malformed tags are encountered. Experimental, use at your own risk.
--keep_sum	string	Keep vector sum constant when splitting multiallelics (see github issue #360).
--multiallelics -m	string	Split multiallelics (-) or join biallelics (+), type: snps, indels, both, any [default: both].
--no_version	boolean_true	Do not append version and command line information to the header.
--do_not_normalize -N	boolean_true	Do not normalize indels (with -m or -c s).
--output_type --O	string	Output type: u: uncompressed BCF z: compressed VCF b: compressed BCF v: uncompressed VCF
--old_rec_tag	string	Annotate modified records with INFO/STR indicating the original variant.
--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>-").
--site_win -w	integer	Buffer for sorting lines that changed position during realignment.
--strict_filter -s	boolean_true	When merging (-m+), merged site is PASS only if all sites being merged PASS.
--targets -t	string	Similar to --regions but streams rather than index-jumps.
--targets_file -T	file	Similar to --regions_file but streams rather than index-jumps.
--targets_overlap	string	Include if POS in the region (0), record overlaps (1), variant overlaps (2). Similar to --regions_overlap.

Name

Type & Properties

--atomize

-a

boolean_true

--atom_overlaps

string

--check_ref

-c

string

--remove_duplicates

-d

string

--fasta_ref

-f

file

--force

boolean_true

--keep_sum

string

--multiallelics

-m

string

--no_version

boolean_true

--do_not_normalize

-N

boolean_true

--output_type

--O

string

--old_rec_tag

string

--regions

--r

string

--regions_file

--R

file

--regions_overlap

string

--site_win

-w

integer

--strict_filter

-s

boolean_true

--targets

-t

string

--targets_file

-T

file

--targets_overlap

string