Philip Mabon

VCF with both SNV and non SNV's

3

I am looking to have both SNV called and non SNV's in the same vcf for downstream analyses. My temporary workaround at the moment is to run the tool twice,...

Include deletion events in VCF

3

Hey was curious to know if deletion events will be included when calculation both AF and COV values in VCF? Below is an example where I would probably not call...

Automate determining coverage minimum and maximum coverage

4

Instead of asking end user for these values, we should determine genome coverage based on the reads themselves.

Available in bioconda and/or Galaxy?

9

Is there any plan in putting BIGSI into [bioconda](https://bioconda.github.io/) for ease of installation and/or into [Galaxy platform](https://usegalaxy.org/) ?

Cannot parse strain name when '.' in file path

3

So the following [line](https://github.com/katholt/srst2/blob/master/scripts/srst2.py#L453) keeps failing when one or more '.' are found on the path to pileup file. Example failing file path is /Storage/galaxy-17.05/working/dapE_11.out__Strain1.dataset_357596.pileup

Website localization

7

Possible we can add support for language localization for non template values? My assumption that need one template for each language that we support. example: MPX_French MPX_English

Feature request: Hidden slots & values when exporting

1

Is it possible in schema_enums/schema_slots tsv files that you can have a hidden column(s) with default value(s) that are sent when an user clicks on export/save as? Example : Column...