It is not currently clear to users of TheiaEuk if a mutation in an antimicrobial resistance gene was not detected (i.e. the reference sequence was detected for an AMR gene) or if there was simply poor coverage of the gene which prevented variant calling. It is technically possible, but very tedious, to answer that question currently. We could improve access by outputting the reference coverage of the resistance genes that TheiaEuk queries for in the snippy_gene_query_task.
It could also be beneficial to report the following metrics as part of the snippy variants task:
number of reads mapped
percent of reads mapped
percent reference coverage and/or depth of coverage
:cool:
:pushpin: Explain the Request
It is not currently clear to users of TheiaEuk if a mutation in an antimicrobial resistance gene was not detected (i.e. the reference sequence was detected for an AMR gene) or if there was simply poor coverage of the gene which prevented variant calling. It is technically possible, but very tedious, to answer that question currently. We could improve access by outputting the reference coverage of the resistance genes that TheiaEuk queries for in the snippy_gene_query_task.
It could also be beneficial to report the following metrics as part of the snippy variants task:
:books: Context
:chart_with_upwards_trend: Desired Behavior
:information_source: Additional Information