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Update readme #81

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Jan 4, 2023
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Update readme #81

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add --panel_filters to readme
jethror1 Jan 4, 2023
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readme
jethror1 Jan 4, 2023
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jethror1 Jan 4, 2023
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Expand Up @@ -118,6 +118,7 @@ The `coverage_report_single.py` script generates the full HTML report. It requir
-p / --panel: panel bed file used for initial annotation, name will be displayed in summary of report (optional)
-l / --limit: number of genes at which to limit including full gene plots, large numbers of genes may take a long time to generate the plots (optional)
-m / --summary: boolean flag to add clinical report summary text in summary section, includes list of all genes with transcripts (optional; default False)
--panel_filters: preset filters of genes / transcripts to set for the full gene plots, these will be presented in a drop down menu for filtering the plots. These should be passed as key:value pairs of panel name to display in the drop down and a comma separated list of gene symbols to filter with (i.e. panel1:gene1,gene2,gene3...) (optional)
--cores: Number of CPU cores to utilise, for larger numbers of genes this will drastically reduce run time. If not given will use maximum available


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