Description

Collects whole genome quality metrics from a bam file

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

bam{:bash}

:file

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

bai{:bash}

:file

Index of th sorted BAM/CRAM/SAM file

*.{bai,crai,sai}

meta2{:bash}

:map

Groovy Map containing reference information e.g. [ id:'test' ]

fasta{:bash}

:file

Genome fasta file

*.{fa,fasta}

meta3{:bash}

:map

Groovy Map containing reference information e.g. [ id:'test' ]

fai{:bash}

:file

Index of the genome fasta file

*.fai

meta4{:bash}

:map

Groovy Map containing reference information e.g. [ id:'test' ]

intervals_list{:bash}

:file

intervals

Output

name:type
description
pattern

wgs_metrics{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.txt{:bash}

:file

File containing the information about mean base quality score for each sequencing cycle

*.txt

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
raredisease
maintainer
Github user ramprasadn
get in touch
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