Description

Splits reads that contain Ns in their cigar string

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:list

BAM/SAM/CRAM file containing reads

*.{bam,sam,cram}

bai{:bash}

:list

BAI/SAI/CRAI index file (optional)

*.{bai,sai,crai}

intervals{:bash}

:file

Bed file with the genomic regions included in the library (optional)

meta2{:bash}

:map

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

fasta{:bash}

:file

The reference fasta file

*.fasta

meta3{:bash}

:map

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

fai{:bash}

:file

Index of reference fasta file

*.fasta.fai

meta4{:bash}

:map

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

dict{:bash}

:file

GATK sequence dictionary

*.dict

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:file

Output file with split reads (BAM/SAM/CRAM)

*.{bam,sam,cram}

*.bam{:bash}

:file

Output file with split reads (BAM/SAM/CRAM)

*.{bam,sam,cram}

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
rnadnavarrnavar
maintainer
Github user kevinmenden
get in touch
Ask a question on Slack Open an issue on GitHub