bcftools/bcftools_concat

Concatenate

VCF

BCF

Description

Concatenate or combine VCF/BCF files. All source files must have the same sample
columns appearing in the same order. The program can be used, for example, to
concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel
VCF into one. The input files must be sorted by chr and position. The files
must be given in the correct order to produce sorted VCF on output unless
the -a, --allow-overlaps option is specified. With the --naive option, the files
are concatenated without being recompressed, which is very fast.

Type

bash_script

License

MIT/Expat, GNU

Keywords

Concatenate

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 v0.4.0 \  
  -main-script target/nextflow/bcftools/bcftools_concat/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file multiple	Input VCF/BCF files to concatenate. All source files must have the same sample columns appearing in the same order. Files must be sorted by chr and position.
--file_list -f	file	Read the list of VCF/BCF files from a file, one file name per line. Alternative to providing multiple --input files.

Name

Type & Properties

--input

-i

file

multiple

--file_list

-f

file

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
--allow_overlaps -a	boolean_true	First coordinate of the next file can precede last record of the current file. Allows overlapping records between files during concatenation.
--compact_ps -c	boolean_true	Do not output PS tag at each site, only at the start of a new phase set block. Reduces output size for phased data.
--rm_dups -d	string	Output duplicate records present in multiple files only once. Options: - `snps`: Remove duplicate SNPs - `indels`: Remove duplicate indels - `both`: Remove duplicate SNPs and indels - `all`: Remove all duplicates - `exact`: Remove exact duplicates only
--remove_duplicates -D	boolean_true	Alias for --rm_dups exact. Remove exact duplicate records present in multiple files.
--drop_genotypes -G	boolean_true	Drop individual genotype information. Removes all sample-specific data from output.
--ligate -l	boolean_true	Ligate phased VCFs by matching phase at overlapping haplotypes. Connects phase information across files.
--ligate_force	boolean_true	Ligate even non-overlapping chunks, keep all sites. Forces ligation without requiring overlap validation.
--ligate_warn	boolean_true	Drop sites in imperfect overlaps. Conservative ligation that removes problematic sites.
--no_version	boolean_true	Do not append version and command line to the header. Produces cleaner output headers.
--naive -n	boolean_true	Concatenate files without recompression. Very fast operation with header compatibility check.
--naive_force	boolean_true	Same as --naive, but header compatibility is not checked. Warning: Dangerous option, use with caution.
--output_type -O	string	Output type and compression level. Options: - `u`: uncompressed BCF - `b`: compressed BCF - `v`: uncompressed VCF - `z`: compressed VCF (with optional compression level 0-9)
--min_pq -q	integer	Break phase set if phasing quality is lower than specified value. Only relevant when working with phased data.
--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
--verbosity -v	integer	Set verbosity level. Controls amount of diagnostic output.
--write_index -W	string	Automatically index the output files. Format: Specify index format or use default.

Name

Type & Properties

--allow_overlaps

-a

boolean_true

--compact_ps

-c

boolean_true

--rm_dups

-d

string

--remove_duplicates

-D

boolean_true

--drop_genotypes

-G

boolean_true

--ligate

-l

boolean_true

--ligate_force

boolean_true

--ligate_warn

boolean_true

--no_version

boolean_true

--naive

-n

boolean_true

--naive_force

boolean_true

--output_type

-O

string

--min_pq

-q

integer

--regions

-r

string

--regions_file

-R

file

--regions_overlap

string

--verbosity

-v

integer

--write_index

-W

string