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

]

vcfs (files)

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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

vcf (file)

The merged VCF file

*.vcf
included in
variantbenchmarking
maintainer
Github user nvnieuwk
get in touch
Ask a question on Slack Open an issue on GitHub

Tools