call variant and sequencing depth information of the variant
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam:file
Sorted BAM file
*.bam
fasta:file
The reference sequence used for mapping and generating the BAM file
*.fa
variants
*.variants.tsv:file
File containing identified variants in a gff-like format
*.variants.tsv
*.depth.tsv:file
versions
versions.yml:file
File containing software versions
versions.yml
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
