vcf_filter_survivor_bcftools

Filter a VCF file of structural variants with SURVIVOR and/or bcftools, and return the result as a bgzipped, tabixed VCF. Note that the nextflow.config shipped with this subworkflow must be included for it to work properly.

filtervcfstructural variantssurvivorbcftools

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/vcf_filter_survivor_bcftools

Description

Input

name

description

pattern

`ch_vcf`

The input channel containing the VCF files to filter and, optionally,
BED files with regions to ignore (pattern: “*.bed”). Pass an empty list
for the BED file to filter genome-wide.

Structure: [ val(meta), path(vcf), path(bed) ]

*.{vcf,vcf.gz}

`minsv`

Min SV size passed to SURVIVOR filter (-1 to disable), ignored if “survivor” is not in val_tools_to_use

`maxsv`

Max SV size passed to SURVIVOR filter (-1 to disable), ignored if “survivor” is not in val_tools_to_use

`minallelefreq`

Min allele frequency passed to SURVIVOR filter (0-1), ignored if “survivor” is not in val_tools_to_use

`minnumreads`

Min number of reads supporting the SV passed to SURVIVOR filter (-1 to disable), ignored if “survivor” is not in val_tools_to_use

`val_tools_to_use`

The filtering tools to run, one or more of: ‘[“survivor”, “bcftools”]’.
SURVIVOR filters on size, allele frequency, read support and regions to
ignore; bcftools filter applies expressions passed to its ext.args.

Output

name

description

pattern

`vcf`

Channel containing the filtered VCF files

Structure: [ val(meta), path(vcf.gz) ]

*.vcf.gz

`tbi`

Channel containing the indices of the filtered VCF files

Structure: [ val(meta), path(tbi) ]

*.tbi

`vcf_tbi`

Channel containing the filtered VCF files and their indices

Structure: [ val(meta), path(vcf.gz), path(tbi) ]

*.{vcf.gz,tbi}