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: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
baf
*.baf.txt.gz:file
The created BAF file
*.baf.txt.gz
baf_tbi
*.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
Genome Analysis Toolkit (GATK4)
