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PT-2883

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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Activity

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Veronika Koltunova
October 29, 2016, 11:07 AM

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

Veronika Koltunova
October 29, 2016, 2:47 PM

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

Marta Girdea
October 30, 2016, 11:47 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, 1:08 PM

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?

Fixed

Assignee

Veronika Koltunova

Reporter

Marta Girdea

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Priority

Major