modules/svanalyzer_svbenchmark

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.

structural variantsvbenchmarking

https://github.com/nf-core/modules/[...]/modules/nf-core/svanalyzer/svbenchmark

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' ]

`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}

`bed:file`

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

*.{bed}

`meta2:map`

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

`fasta:file`

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

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

`meta3:map`

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

`fai:file`

The reference FASTA index file

*.{fai}

Output

name:type

description

pattern