Pedigree visualization not showing affected status

[mvelinder]

Should be shading/filling the circle/square for the affected individual in the pedigree

And the same for any other affected individuals in the family

[WilliamRichards2017]

@mvelinder This is because I gave Adit a ped file with an unknown affection status. Affection status appears to be displaying properly when given a ped file with an affection status of 2. This can be verified on dev.clin.iobio.io using the following urls, and the attatched .ped file https://s3.amazonaws.com/iobio/samples/vcf/platinum-exome.vcf.gz https://s3.amazonaws.com/iobio/samples/bam/NA12878.exome.bam testPed.txt

[mvelinder]

Tried to test this, but have been stuck on for at least 10 minutes now.

Is dev.clin working for you @WilliamRichards2017 ?

[WilliamRichards2017]

@mvelinder Yeah it's working for me

Could you open up the console and screenshot any error messages you might be recieving

[adityaekawade]

Hi @mvelinder , is it working for you now? Did you add data for all these inputs: VCF, samples, BAM, Gene sets, PED? The page might be stuck if any of the above fields are missing,

[mvelinder]

@adityaekawade I've only added the VCF and then clicked Next. If we are going to require the BAM too I'd suggest keeping Next grayed out until the BAM has been loaded.

Or we could allow them to load it without the BAM, but that sort of diminishes the "comprehensive" nature of the app. Any thoughts @AlistairNWard ?

[adityaekawade]

I have grayed out the "Next" button until both VCF and BAM are added.

[mvelinder]

That's a good enough solution for now I think @adityaekawade

[AlistairNWard]

I agree, we are trying to be comprehensive, so require all files, so this works for me. If you just want to jump in with a vcf, you can use gene.