lofreq/lofreq_indelqual
bam
indel
qualities
indelqual
lofreq
lofreq/indelqual
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!
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Input BAM file. |
--ref -f | file | Reference sequence used for mapping (Only required for --dindel). |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--out -o | file required output | Output BAM file. |
Arguments
Name | Type & Properties | Description |
|---|---|---|
--uniform -u | string | Add this indel quality uniformly to all bases. Use two comma separated values to specify insertion and deletion quality separately. (clashes with --dindel). |
--dindel | boolean_true | Add Dindel's indel qualities (Illumina specific) (clashes with -u; needs --ref). |
--verbose | boolean_true | Be verbose. |
Run this component
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 v0.3.0 \
-main-script target/nextflow/lofreq/lofreq_indelqual/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
lofreq/lofreq_indelqualbiobox v0.3.0
Uses
0 relationships
No component dependencies found.