EXPERIMENTAL TOOL! Convert SiteDepth to BafEvidence
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
site_depths
:file
Files containing site depths
*.sd.txt.gz
site_depths_indices
The indices of the site depth files
*.sd.txt.gz.tbi
vcf
Input VCF of SNPs marking loci for site depths
*.vcf.gz
tbi
Index of the input VCF of SNPs marking loci for site depths
*.vcf.gz.tbi
fasta
The reference FASTA file
*.{fasta,fa}
fasta_fai
The index of the reference FASTA file
*.fai
dict
The sequence dictionary of the reference FASTA file
*.dict
baf
*.baf.txt.gz
The created BAF file
baf_tbi
*.baf.txt.gz.tbi
The index of the created BAF file
versions_gatk4
${task.process}
:string
The name of the process
gatk4
The name of the tool
gatk --version | sed -n '/GATK.*v/s/.*v//p'
:eval
The expression to obtain the version of the tool
versions
Genome Analysis Toolkit (GATK4)
