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theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
GNU General Public License v3.0
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Snippy_Variants: Calculate % reads aligned #477

Open emmadoughty opened 1 month ago

emmadoughty commented 1 month ago

:cool:

:pushpin: Explain the Request

Please add output for % reads aligned for Anippy_Variants

:books: Context

Currently, Snipy_Variants provides an output column of # reads aligned, but this isn't put in context of the total number of reads in the sample. It would be very helpful to have a % calculated to be able to see if there are any major differences in the samples vs the ref, or any contamination indicated by low % reads aligned.

:chart_with_upwards_trend: Desired Behavior

Add extra output column with %reads aligned

:information_source: Additional Information