Description

Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector collects read information that is used by Dedup which in turn marks or removes duplicate reads.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing reference information.
e.g. [ id:‘test’, single_end

]

bam (file)

BAM file.

*.bam

bai (file)

BAI file

*.bai

meta2 (map)

Groovy Map containing reference information.
e.g. [ id:‘test’, single_end

]

fasta (file)

Genome fasta file

*.{fa,fasta}

meta3 (map)

Groovy Map containing reference information.
e.g. [ id:‘test’, single_end

]

fasta_fai (file)

The index of the FASTA reference.

*.fai

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing reference information.
e.g. [ id:‘test’, single_end

]

cram (file)

CRAM file

*.cram

crai (file)

CRAM index file

*.crai

bam (file)

BAM file.

*.bam

bai (file)

BAI file

*.bai

score (file)

The score file indicates which reads LocusCollector finds are likely duplicates.

*.score

metrics (file)

Output file containing Dedup metrics incl. histogram data.

*.metrics

metrics_multiqc_tsv (file)

Output tsv-file containing Dedup metrics excl. histogram data.

*.metrics.multiqc.tsv

versions (file)

File containing software versions

versions.yml
included in
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maintainer
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Tools

sentieon

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon.com