Description

SVbenchmark compares a set of “test” structural variants in VCF format to a known truth set (also in VCF format) and outputs estimates of sensitivity and specificity.

Input

Name (Type)
Description
Pattern

meta (map)

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

meta2 (map)

Groovy Map containing reference genome information for fasta
e.g. [ id:'test2' ]

meta3 (map)

Groovy Map containing reference genome information for fai
e.g. [ id:'test3' ]

test (file)

A VCF-formatted file of structural variants to test (required)

*.{vcf,vcf.gz}

test_tbi (file)

A VCF-formatted file index of structural variants to test only for zipped files

*.{vcf.gz.tbi}

truth (file)

A VCF-formatted file of variants to compare against (required)

*.{vcf,vcf.gz}

truth_tbi (file)

A VCF-formatted file of variants to compare against only for zipped files

*.{vcf.gz.tbi}

fasta (file)

The reference FASTA file for the supplied VCF file or files (required)

*.{fa,fasta,fa.gz,fasta.gz}

bed (file)

BED File of regions from which to include variants. Used to filter both test and truth variants.

*.{bed}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information inherited from test vcf
e.g. [ id:'test']

versions (file)

File containing software versions

versions.yml

fns (file)

VCF file with False Negatives

*.{vcf.gz}

fps (file)

VCF file with False Positives

*.{vcf.gz}

distances (file)

TSV file with genomic distances and size differences between structural variants compared

*.{distances}

log (file)

LOG file of the run

*.{log}

report (file)

Text file reporting RECALL, PRECISION and F1.

*.{report}
included in
variantbenchmarking
maintainer
Github user kubranarci
get in touch
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Tools

svanalyzer

SVanalyzer: tools for the analysis of structural variation in genomes

svanalyzer.readthedocs.io/en/latest https://github.com/nhansen/SVanalyzer