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.

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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