Description

Performs tests on BAF files

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bed (file)

A BED file created with svtk vcf2bed

*.bed

baf (file)

A BAF file created with gatk PrintSVEvidence

*.baf.txt.gz

baf_index (file)

The index of the BAF file

*.baf.txt.gz.tbi

batch (file)

A text file containing information about the sample(s)

*.txt

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

metrics (file)

The results file from the BAF test

*.metrics
author
Github user nvnieuwk
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Tools

svtk
MIT

Utilities for consolidating, filtering, resolving, and annotating structural variants.

github.com/broadinstitute/gatk-sv[...]src/svtk