Description

Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

meta2 (map)

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

meta3 (map)

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

input (file)

BAM/CRAM file.

*.{bam,cram}

index (file)

BAI/CRAI file.

*.{bai,crai}

fasta (file)

Genome fasta file

*.{fa,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

]

output (file)

BAM/CRAM file

*.{bam,cram}

index (file)

BAM/CRAM index file

*.{bai,crai}

output_index (file)

BAM/CRAM alignment and the corresponding index file

versions (file)

File containing software versions

versions.yml
included in
raredisease
maintainer
Github user ramprasadn
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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