Description

Performs fastq alignment to a fasta reference using Sentieon’s BWA MEM

Input

Name (Type)
Description
Pattern

meta (map)

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

]

reads (file)

Genome fastq files (single-end or paired-end)

meta2 (map)

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

]

index (file)

BWA genome index files

*.{amb,ann,bwt,pac,sa}

meta3 (map)

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

]

fasta (file)

Genome fasta file

*.{fa,fasta}

meta4 (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

]

bam (file)

BAM file.

*.bam

bai (file)

BAI file

*.bai

versions (file)

File containing software versions

versions.yml
included in
raredisease sarek
maintainers
Github user asp8200
Github user DonFreed
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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