# Coverage and frequency requirements for variants in FASTA output from the DRAGEN COVID Lineage app

**What are the minimum coverage and Variant Frequency (VF) requirements to include a variant in the consensus sequence FASTA file output in DRAGEN COVID Lineage app?**

The DRAGEN COVID Lineage app on BaseSpace can be used to generate a consensus sequence in FASTA format.

To do this, detected sequence variants that meet the following criteria are ingrained into the SARS-CoV-2 reference sequence (NCBI Accession NC\_045512.2).

1. Variant Frequency (VF) >= 0.5
2. Coverage >10X (by default): This threshold can be modified by changing the 'Callability Threshold' parameter while launching the app.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-a5a204ed30246d0851584ccbded2484fdfe7ad28%2Fimage1.png?alt=media\&token=e86c65cb-9f23-4ace-a5fd-9592e11f5835)

**Note**: This requirement only applies to the \\\*.consensus\_hard\_masked\_sequence.fa file\
For the consensus\_soft\_masked\_sequence.fa. The variants that have VF < 0.5 and Coverage <10X will be called as Ref, while in the consensus\_hard\_masked\_sequence.fa, these positions are called as 'N'.

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