EXPERIMENTAL TOOL! Convert SiteDepth to BafEvidence
meta
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
site_depths
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
versions
File containing software versions
versions.yml
baf
The created BAF file
*.baf.txt.gz
baf_tbi
The index of the created BAF file
*.baf.txt.gz.tbi
Genome Analysis Toolkit (GATK4)
