Description

Calculates the allele-specific read counts for allele-specific expression analysis of RNAseq data

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM file

*.{bam}

bai{:bash}

:file

index file for BAM file

*.{bai}

vcf{:bash}

:file

VCF file

*.{vcf.gz}

tbi{:bash}

:file

index file for VCF file

*.{vcf.gz.tbi}

meta2{:bash}

:map

Groovy Map containing reference information e.g. [ id:'reference' ]

fasta{:bash}

:file

fasta file

*.{fasta,fa}

meta3{:bash}

:map

Groovy Map containing reference information e.g. [ id:'reference' ]

fai{:bash}

:file

fasta index file

*.{fai}

meta4{:bash}

:map

Groovy Map containing reference information e.g. [ id:'reference' ]

dict{:bash}

:file

dictionary file

*.{dict}

intervals{:bash}

:file

interval file

Output

name:type
description
pattern

csv{:bash}

meta{:bash}

:map

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

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
maintainer
Github user Lucpen
get in touch
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