Description

WARNING - this tool is still experimental and shouldn’t be used in a production setting. Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.

Input

name:type
description
pattern

meta

:map

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

evidence_files

:file

The evidence files created by CollectSVEvidence. They all need to be of the same type to print the SV evidence.

*.{pe,sr,baf,rd}.txt(.gz)

evidence_indices

:file

The indices of the evidence files created by CollectSVEvidence

*.{pe,sr,baf,rd}.txt(.gz).tbi

bed

:file

An optional BED file

*.bed

fasta

:file

An optional reference FASTA file

*.{fa,fasta}

fasta_fai

:file

An optional reference FASTA file index

*.fai

dict

:file

The mandatory sequence dictionary file

*.dict

Output

name:type
description
pattern

printed_evidence

meta

:map

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

*.txt.gz

:file

The output file containing the discordant read pairs or the soft clipped reads

*.{pe,sr,baf,rd}.txt.gz

printed_evidence_index

meta

:map

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

*.txt.gz.tbi

:file

The index file of the output compressed text file containing the discordant read pairs or the soft clipped reads

*.{pe,sr,baf,rd}.txt.gz.tbi

versions_gatk4

${task.process}

:string

The name of the process

gatk4

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

gatk4

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'

: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 nvnieuwk
get in touch
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