Description

Print reads in the SAM/BAM/CRAM 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/SAM file

*.{bam,cram,sam}

index{:bash}

:file

BAM/CRAM/SAM file

*.{bai,crai,sai}

meta2{:bash}

:map

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

fasta{:bash}

:file

reference fasta file

*.{fa,fasta}

meta3{:bash}

:map

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

fai{:bash}

:file

reference fasta index file

*.{fai}

meta4{:bash}

:map

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

dict{:bash}

:file

reference fasta dictionary file

*.{dict}

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

${prefix}.bam{:bash}

:file

Sorted BAM file

*.{bam}

cram{:bash}

meta{:bash}

:map

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

${prefix}.cram{:bash}

:file

Sorted CRAM file

*.{cram}

sam{:bash}

meta{:bash}

:map

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

${prefix}.sam{:bash}

:file

Sorted SAM file

*.{sam}

versions_gatk4{:bash}

${task.process}{:bash}

:string

The name of the process

gatk4{:bash}

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

gatk4{:bash}

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'{:bash}

:eval

The expression to obtain the version of the tool

Tools

gatk4
Apache-2.0

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s 10.1158/1538-7445.AM2017-3590
included in
rarediseasevariantcatalogue
maintainer
Github user ramprasadn
get in touch
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