Description

EXPERIMENTAL TOOL! Convert SiteDepth to BafEvidence

Input

name:type
description
pattern

meta:map

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

]

site_depths:file

Files containing site depths

*.sd.txt.gz

site_depths_indices:file

The indices of the site depth files

*.sd.txt.gz.tbi

vcf:file

Input VCF of SNPs marking loci for site depths

*.vcf.gz

tbi:file

Index of the input VCF of SNPs marking loci for site depths

*.vcf.gz.tbi

fasta:file

The reference FASTA file

*.{fasta,fa}

fasta_fai:file

The index of the reference FASTA file

*.fai

dict:file

The sequence dictionary of the reference FASTA file

*.dict

Output

name:type
description
pattern

baf

meta:map

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

]

*.baf.txt.gz:file

The created BAF file

*.baf.txt.gz

baf_tbi

meta:map

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

]

*.baf.txt.gz.tbi:file

The index of the created BAF file

*.baf.txt.gz.tbi

versions

versions.yml:file

File containing software versions

versions.yml