Description

Compare or merge VCF files to generate a consensus or multi sample VCF files.

Input

name:type
description
pattern

meta{:bash}

:map

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

vcfs{:bash}

:list

The VCF files to be merged Gzipped VCF files are not supported: https://github.com/fritzsedlazeck/SURVIVOR/issues/158

*.vcf

max_distance_breakpoints{:bash}

:integer

Max distance between breakpoints (0-1 percent of length, 1- number of bp)

min_supporting_callers{:bash}

:integer

Minimum number of supporting caller

account_for_type{:bash}

:integer

Take the type into account (1==yes, else no)

account_for_sv_strands{:bash}

:integer

Take the strands of SVs into account (1==yes, else no)

estimate_distanced_by_sv_size{:bash}

:integer

Estimate distance based on the size of SV (1==yes, else no)

min_sv_size{:bash}

:integer

Minimum size of SVs to be taken into account

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf{:bash}

:file

The merged VCF file

*.vcf

versions_survivor{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

survivor{:bash}

:string

The name of the tool

SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

survivor{:bash}

:string

The name of the tool

SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
variantbenchmarking
maintainer
Github user nvnieuwk
get in touch
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