Snippy not identifying rRNA SNPs (presumably due to conserved region?)

[BGemler]

Hello,

We are not identifying known SNPs near the 3' end of rRNA in Flavobacterium johnsoniae - we confirmed that the SNPs were present in every sample/relevant read by examining mapped reads. We assume that snippy doesn't identify SNPs here because the reads will be multimapped to all 16S rRNA copies in the genome - is there a flag or approach that allows multimapped reads to be carried through in SNP analysis?

Thank you for your efforts and tool!