vcf_extract_relate_somalier

Perform somalier extraction and relate stats on input VCFs

somalierstatsvcfpedrelatedness

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

Description

Perform somalier extraction and relate stats on input VCFs

Input

name:type

description

pattern

`ch_vcfs`

The input VCFs to perform the stats on, optionally with their indices.
This channel can also contain the number of samples in the same family/group
to check relatedness. This is advised to add as it can improve the efficiency of your pipeline
Structure: [ val(meta), path(vcf), path(tbi), val(count) ]

`ch_fasta`

The reference FASTA used to create the VCF files
Structure: [ path(fasta) ]

`ch_fasta_fai`

The index of the reference FASTA
Structure: [ path(fasta_fai) ]

`ch_somalier_sites`

A VCF containing the common sites for Somalier
Structure: [ path(somalier_sites_vcf) ]

`ch_peds`

A channel containing an optional PED file for the corresponding families. This channel has to be given, but can be like [meta, []].
When you don’t want to use a PED file, you must supply a channel
containing the meta and an empty value ([]) instead of a PED
Structure: [ val(meta), path(ped) ]

`ch_sample_groups`

Optional - A text file describing how the samples should be grouped
Structure: [ path(txt) ]

`val_common_id`

Optional - A common identifier in the meta map.
This will be used to determine which VCFs should be used in somalier_relate.
This value should be given when using single sample VCFs

Output

name:type

description

pattern

`extract`

The extract file created with Somalier extract
Structure: [ val(meta), path(extract) ]

`html`

An HTML file containing an interactive graph on the relatedness of the samples
Structure: [ val(meta), path(html) ]

`pairs_tsv`

A TSV file detailing the relatedness between pairs of samples
Structure: [ val(meta), path(tsv) ]

`samples_tsv`

A TSV file detailing the relatedness between all samples with the same meta
Structure: [ val(meta), path(tsv) ]

`versions`

Files containing software versions
Structure: [ path(versions.yml) ]