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