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

]

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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

printed_evidence (file)

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

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

printed_evidence (file)

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

*.{pe,sr,baf,rd}.txt.gz.tbi
maintainer
Github user nvnieuwk
get in touch
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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