This workflow aims at generating reliable consensus sequences from variant calls according to transparent criteria that capture at least some of the complexity of variant calling.
It takes a collection of VCFs (with DP and DP4 INFO fields) and a collection of the corresponding aligned reads (for the purpose of calculating genome-wide coverage) such as produced by any of the variant calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates a collection of viral consensus sequences and a multisample FASTA of all these sequences.
Each consensus sequence is guaranteed to capture all called, filter-passing (as per the FILTER column of the VCF input) variants found in the VCF of its sample that reach a user-defined consensus allele frequency threshold.
Filter-failing variants and variants below a second user-defined minimal allele frequency threshold will be ignored.
Genomic positions of filter-passing variants with an allele frequency in between the two thresholds will be hard-masked (with N) in the consensus sequence of their sample.
Genomic positions with a coverage (calculated from the read alignments input) below another user-defined threshold will be hard-masked, too, unless they are consensus variant sites.