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{:bash}

:map

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

input{:bash}

:file

BAM/CRAM file.

*.{bam,cram}

index{:bash}

:file

BAI/CRAI file.

*.{bai,crai}

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

The index of the FASTA reference.

*.fai

Output

name:type
description
pattern

output{:bash}

meta{:bash}

:map

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

${prefix}{:bash}

:file

BAM/CRAM file. Depends on how ext.prefix is set. BAM “ext.prefix = .bam”, CRAM “ext.prefix = .cram”. Defaults to cram

*.{bam,cram}

index{:bash}

meta{:bash}

:map

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

${prefix}.${index}{:bash}

:file

BAM/CRAM index file

*.{bai,crai}

output_index{:bash}

meta{:bash}

:map

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

${prefix}{:bash}

:file

BAM/CRAM file. Depends on how ext.prefix is set. BAM “ext.prefix = .bam”, CRAM “ext.prefix = .cram”. Defaults to cram

*.{bam,cram}

${prefix}.${index}{:bash}

:file

BAM/CRAM index file

*.{bai,crai}

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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