Description

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

Input

name:type
description
pattern

meta:map

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

vcfs:list

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

*.vcf

max_distance_breakpoints:integer

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

min_supporting_callers:integer

Minimum number of supporting caller

account_for_type:integer

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

account_for_sv_strands:integer

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

estimate_distanced_by_sv_size:integer

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

min_sv_size:integer

Minimum size of SVs to be taken into account

Output

name:type
description
pattern

vcf

meta:map

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

*.vcf:file

The merged VCF file

*.vcf

versions

versions.yml:file

File containing software versions

versions.yml

Tools

included in
variantbenchmarking
maintainer
Github user nvnieuwk
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