Bcftools

Filter the variants called by freebayes or cellSNP

Info

ID: bcftools
Namespace: genetic_demux

Links

Source

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.2 -latest \
  -main-script target/nextflow/genetic_demux/bcftools/main.nf \
  --help

Run command

Example of params.yaml

# Arguments
vcf: # please fill in - example: ["path/to/file"]
concat: false
filter: false
filter_qual: 30
# output: "$id.$key.output.output"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.2 -latest \
  -profile docker \
  -main-script target/nextflow/genetic_demux/bcftools/main.nf \
  -params-file params.yaml

Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument group

Arguments

Name	Description	Attributes
--vcf	VCF files, must have the same sample columns appearing in the same order.	List of file, required, multiple_sep: ";"
--concat	Concatenate or combine VCFs and sort them.	boolean_true
--filter	Filter VCFs.	boolean_true
--filter_qual	Filter VCFs with specified QUAL threshold.	integer, default: 30
--output	bcftools output directory	file, example: "bcftools_out"

Authors

• Xichen Wu (author)