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:false ]

input:file

BAM/CRAM file.

*.{bam,cram}

index:file

BAI/CRAI file.

*.{bai,crai}

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

The index of the FASTA reference.

*.fai

Output

name:type
description
pattern

output

meta:map

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

${prefix}: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

meta:map

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

${prefix}.${index}:file

BAM/CRAM index file

*.{bai,crai}

output_index

meta:map

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

${prefix}:file

BAM/CRAM alignment and the corresponding index file

${prefix}.${index}:file

BAM/CRAM alignment and the corresponding index file

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
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