Description

Collects whole genome quality metrics from a bam file

Input

name:type
description
pattern

meta:map

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

bam:file

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

bai:file

Index of th sorted BAM/CRAM/SAM file

*.{bai,crai,sai}

meta2:map

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

fasta:file

Genome fasta file

*.{fa,fasta}

meta3:map

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

fai:file

Index of the genome fasta file

*.fai

meta4:map

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

intervals_list:file

intervals

Output

name:type
description
pattern

wgs_metrics

meta:map

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

*.txt:file

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

*.txt

versions

versions.yml: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
Ask a question on Slack Open an issue on GitHub