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