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Possible to set %identity of reads mapping to ref? #573

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appliedmicrobiologyresearch opened this issue Nov 20, 2023 · 0 comments
Open

Possible to set %identity of reads mapping to ref? #573

appliedmicrobiologyresearch opened this issue Nov 20, 2023 · 0 comments

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@appliedmicrobiologyresearch
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Hi there! I would love to use snippy for "mixed" datasets with multiple bacterial genomes in. At the moment I am getting mixed mapping to the rRNA operons. Is there a way of setting this in the bwa part (I'm not sure that --mapqual does what I want?). Or would masking the rRNA operons be a better method? Thanks!
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