I've done variant calling for many eukaryotic organisms, and always followed a simple, highly vetted pipeline of mapping my reads to a reference, generating pileup with samtools, and calling variants with bcftools. Now I'm interested in SNP calling for viral genomes, and although I know of several published papers that use this pipeline in virology, I heard that a haploid-specific algorithm, like that used in FreeBayes may be a more accurate analysis route.
Is this really the case? Does anyone know what negative effects will occur if using bcftools with viral sequence? Are there better options than FreeBayes?
Thanks for any advice.