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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

baf (file)

The created BAF file

*.baf.txt.gz

baf_tbi (file)

The index of the created BAF file

*.baf.txt.gz.tbi