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{:bash}

:map

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

test{:bash}

:file

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

*.{vcf,vcf.gz}

test_tbi{:bash}

:file

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

*.{vcf.gz.tbi}

truth{:bash}

:file

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

*.{vcf,vcf.gz}

truth_tbi{:bash}

:file

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

*.{vcf.gz.tbi}

bed{:bash}

:file

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

*.{bed}

meta2{:bash}

:map

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

fasta{:bash}

:file

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

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

meta3{:bash}

:map

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

fai{:bash}

:file

The reference FASTA index file

*.{fai}

Output

name:type
description
pattern

fns{:bash}

meta{:bash}

:map

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

*.falsenegatives.vcf.gz{:bash}

:file

VCF file with False Negatives

*.{vcf.gz}

fps{:bash}

meta{:bash}

:map

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

*.falsepositives.vcf.gz{:bash}

:file

VCF file with False Positives

*.{vcf.gz}

distances{:bash}

meta{:bash}

:map

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

*.distances{:bash}

:file

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

*.{distances}

log{:bash}

meta{:bash}

:map

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

*.log{:bash}

:file

LOG file of the run

*.{log}

report{:bash}

meta{:bash}

:map

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

*.report{:bash}

:file

Text file reporting RECALL, PRECISION and F1.

*.{report}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

svanalyzer

SVanalyzer: tools for the analysis of structural variation in genomes

svanalyzer.readthedocs.io/en/latest https://github.com/nhansen/SVanalyzer
included in
variantbenchmarking
maintainer
Github user kubranarci
get in touch
Ask a question on Slack Open an issue on GitHub