Add chromosome, start position, end position and reference genome as fields for variants

Description

They should be the first entries in the "extended" set of fields in the following order:

  • reference genome: dropdown with:

    • stored value: GRCh38, displayed value: GRCh38 (hg38)

    • stored value: GRCh37, displayed value: GRCh37 (hg19)

    • stored value: NCBI36, displayed value: NCBI36 (hg18)

  • chromosome: 1, 2, 3,....22, X, Y

  • start position: number

  • end position: number

(see also https://github.com/phenotips/phenotips/blob/master/components/patient-data/ui/src/main/resources/PhenoTips/VCF.xml#L87)

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Veronika Koltunova
October 29, 2016, 12:07 AM

Any preferences about the display position/order of those fields? Or just uppend them under Sanger validation?

Veronika Koltunova
October 29, 2016, 3:47 AM

Also, is it "end position" or "stop position"?

Marta Girdea
October 30, 2016, 12:47 AM

It's "end". Sorry for using the wrong word in the description, I fixed it now.

They should probably be the first entries in the "extended" set of fields. opinions?

Orion Buske
October 30, 2016, 2:08 AM

I agree. The order I would suggest is:
1. reference genome
2. chromosome
3. start
4. end

I'd also suggest ordering the reference genomes in reverse chronological order (38 first, then 37, then 36). , should there be a default selection or should it start as blank?

Assignee

Veronika Koltunova

Reporter

Marta Girdea

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