Description
Insert indel qualities into BAM file (required for indel predictions).
The preferred way of inserting indel qualities should be via GATK's BQSR (>=2) If that's not possible, use this subcommand.
The command has two modes: 'uniform' and 'dindel':
'uniform' will assign a given value uniformly, whereas
'dindel' will insert indel qualities based on Dindel (PMID 20980555).
Both will overwrite any existing values.
Do not realign your BAM file afterwards!
Type
bash_script
License
MIT
Keywords
Contributors
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
out: "$id.$key.out.bam"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.4.1 \
-main-script target/nextflow/lofreq/lofreq_indelqual/main.nf \
-params-file params.yaml Name | Type & Properties |
|---|---|
--input | file required |
--ref -f | file |
Name | Type & Properties |
|---|---|
--out -o | file required output |
Name | Type & Properties |
|---|---|
--uniform -u | string |
--dindel | boolean_true |
--verbose | boolean_true |