Description
Filter the variants called by freebayes or cellSNP
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
filter_qual: [ 30 ]
output: "$id.$key.output.bcftools_out"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v3.0.1 \
-main-script target/nextflow/genetic_demux/bcftools/main.nf \
-params-file params.yaml Name | Type & Properties |
|---|---|
--vcf | file required multiple |
--concat | boolean_true |
--filter | boolean_true |
--filter_qual | integer |
--output | file output |