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.

Inputs

Name	Type & Properties	Description
--input -i	file multiple	Input VCF/BCF files to concatenate.
--file_list -f	file	Read the list of VCF/BCF files from a file, one file name per line.

Name

Type & Properties

--input

-i

file

multiple

--file_list

-f

file

Outputs

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

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.
--compact_PS -c	boolean_true	Do not output PS tag at each site, only at the start of a new phase set block.
--remove_duplicates -d	string	Output duplicate records present in multiple files only once: <snps\|indels\|both\|all\|exact>.
--ligate -l	boolean_true	Ligate phased VCFs by matching phase at overlapping haplotypes.
--ligate_force	boolean_true	Ligate even non-overlapping chunks, keep all sites.
--ligate_warn	boolean_true	Drop sites in imperfect overlaps.
--no_version	boolean_true	Do not append version and command line information to the header.
--naive -n	boolean_true	Concatenate files without recompression, a header check compatibility is performed.
--naive_force	boolean_true	Same as --naive, but header compatibility is not checked. Dangerous, use with caution.
--output_type -O	string	Output type: u: uncompressed BCF z: compressed VCF b: compressed BCF v: uncompressed VCF
--min_PQ -q	integer	Break phase set if phasing quality is lower than <int>.
--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>-").

Name

Type & Properties

--allow_overlaps

-a

boolean_true

--compact_PS

-c

boolean_true

--remove_duplicates

-d

string

--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

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_concat/main.nf \  
  -params-file params.yaml

bcftools/bcftools_concat

Inputs

Outputs

Options

Run this component

Relationships

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