subworkflows/vcf_extract_relate_somalier
Perform somalier extraction and relate stats on input VCFs
Input
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) ]
A VCF containing the common sites for Somalier
Structure: [ path(somalier_sites_vcf) ]
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) ]
Optional - A text file describing how the samples should be grouped
Structure: [ path(txt) ]
Output
An HTML file containing an interactive graph on the relatedness of the samples
Structure: [ val(meta), path(html) ]
A TSV file detailing the relatedness between pairs of samples
Structure: [ val(meta), path(tsv) ]
A TSV file detailing the relatedness between all samples with the same meta
Structure: [ val(meta), path(tsv) ]