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{:bash}

:map

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

bam{:bash}

:file

BAM file.

*.bam

bai{:bash}

:file

BAI file

*.bai

meta2{:bash}

:map

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

fasta{:bash}

:file

Genome fasta file

*.{fa,fasta}

meta3{:bash}

:map

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

fasta_fai{:bash}

:file

The index of the FASTA reference.

*.fai

Output

name:type
description
pattern

cram{:bash}

meta{:bash}

:map

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

*.cram{:bash}

:file

CRAM file

*.cram

crai{:bash}

meta{:bash}

:map

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

*.crai{:bash}

:file

CRAM index file

*.crai

bam{:bash}

meta{:bash}

:map

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

*.bam{:bash}

:file

BAM file.

*.bam

bai{:bash}

meta{:bash}

:map

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

*.bai{:bash}

:file

BAI file

*.bai

score{:bash}

meta{:bash}

:map

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

*.score{:bash}

:file

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

*.score

metrics{:bash}

meta{:bash}

:map

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

*.metrics{:bash}

:file

Output file containing Dedup metrics incl. histogram data.

*.metrics

metrics_multiqc_tsv{:bash}

meta{:bash}

:map

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

*.metrics.multiqc.tsv{:bash}

:file

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

*.metrics.multiqc.tsv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
included in
rarediseasesarek
maintainer
Github user asp8200
get in touch
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