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.gz"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/bcftools/bcftools_norm/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	Input VCF/BCF file. The file to be normalized, left-aligned, and/or processed.

Name

Type & Properties

--input

file

required

Outputs

Name	Type & Properties	Description
--output -o	file required output	Write output to a file. If not specified, output goes to standard output.

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). Breaks down complex variants into simpler components.
--atom_overlaps	string	Use the star allele () for overlapping alleles or set to missing (.). Options:* - `*`: Use star allele for overlaps (default) - `.`: Set overlapping alleles to missing
--check_ref -c	string	Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites. Options: - `e`: exit on REF mismatch (default) - `w`: warn about REF mismatches - `x`: exclude sites with REF mismatches - `s`: set/fix REF mismatches
--remove_duplicates_flag -D	boolean_true	Remove duplicate lines of the same type. Shorthand for --rm_dup exact.
--rm_dup -d	string	Remove duplicate snps\|indels\|both\|all\|exact. Options: - `snps`: Remove duplicate SNPs - `indels`: Remove duplicate indels - `both`: Remove duplicate SNPs and indels - `all`: Remove all duplicates - `exact`: Remove exact duplicates only
--exclude -e	string	Do not normalize records for which the expression is true. Uses bcftools expression syntax (see man page for details).
--fasta_ref -f	file	Reference sequence file. Required for checking REF alleles and left-alignment.
--force	boolean_true	Try to proceed even if malformed tags are encountered. Warning: Experimental feature, use at your own risk.
--gff_annot -g	file	Follow HGVS 3'rule and right-align variants in transcripts on the forward strand. Uses GFF annotation file for transcript information.
--include -i	string	Normalize only records for which the expression is true. Uses bcftools expression syntax (see man page for details).
--keep_sum	string	Keep vector sum constant when splitting multiallelics. Comma-separated list of INFO tags (see github issue #360).
--multiallelics -m	string	Split multiallelics (-) or join biallelics (+), type: snps\|indels\|both\|any. Options: - `-both`: Split multiallelic sites (default) - `+both`: Join biallelic sites - Use `snps`, `indels`, `any` for specific variant types
--multi_overlaps	string	Fill in the reference (0) or missing (.) allele when splitting multiallelics. Options: - `0`: Fill with reference allele (default) - `.`: Fill with missing allele
--no_version	boolean_true	Do not append version and command line to the header. Produces cleaner output headers.
--do_not_normalize -N	boolean_true	Do not normalize indels (with -m or -c s). Skips indel left-alignment and normalization.
--old_rec_tag	string	Annotate modified records with INFO/STR indicating the original variant. Adds specified INFO tag to track original variants.
--output_type -O	string	Output type and compression level. Options: - `u`: uncompressed BCF - `b`: compressed BCF - `v`: uncompressed VCF (default) - `z`: compressed VCF (with optional compression level 0-9)
--regions -r	string	Restrict to comma-separated list of regions. Formats supported: chr\|chr:pos\|chr:beg-end\|chr:beg-[,…]
--regions_file -R	file	Restrict to regions listed in a file. Regions can be specified in VCF, BED, or tab-delimited format.
--regions_overlap	string	Include if POS in the region (0), record overlaps (1), variant overlaps (2). Options: - `0`: POS inside region (default for -t/-T) - `1`: overlapping records included (default for -r/-R) - `2`: true overlapping variation only
--strict_filter -s	boolean_true	When merging (-m+), merged site is PASS only if all sites being merged PASS. Stricter FILTER handling during multiallelic joining.
--sort -S	string	Sort order: chr_pos,lex. Options: - `chr_pos`: Sort by chromosome and position (default) - `lex`: Lexicographic sort
--targets -t	string	Similar to --regions but streams rather than index-jumps. More efficient for processing many small regions.
--targets_file -T	file	Similar to --regions_file but streams rather than index-jumps. More efficient for processing many regions from file.
--targets_overlap	string	Include if POS in the region (0), record overlaps (1), variant overlaps (2). Similar to --regions_overlap but for streaming mode.
--verbosity -v	integer	Verbosity level. Controls amount of diagnostic output.
--site_win -w	integer	Buffer for sorting lines which changed position during realignment. Larger values use more memory but handle more complex rearrangements.
--write_index -W	string	Automatically index the output files. Format: Specify index format or use default.

Name

Type & Properties

--atomize

-a

boolean_true

--atom_overlaps

string

--check_ref

-c

string

--remove_duplicates_flag

-D

boolean_true

--rm_dup

-d

string

--exclude

-e

string

--fasta_ref

-f

file

--force

boolean_true

--gff_annot

-g

file

--include

-i

string

--keep_sum

string

--multiallelics

-m

string

--multi_overlaps

string

--no_version

boolean_true

--do_not_normalize

-N

boolean_true

--old_rec_tag

string

--output_type

-O

string

--regions

-r

string

--regions_file

-R

file

--regions_overlap

string

--strict_filter

-s

boolean_true

--sort

-S

string

--targets

-t

string

--targets_file

-T

file

--targets_overlap

string

--verbosity

-v

integer

--site_win

-w

integer

--write_index

-W

string