elimuinformatics/vcf2fhir

genetic variant assessment should be 'absent' when GT=0/0

Closed this issue · 3 comments

Yun-00 commented

Dear Authors of vcf2fhir,

In the current design of vcf2fhir, Observation-variant includes a fixed content 'LOINC 69548-6'.
However, it would not be logical to convert the record this way when GT=0/0.
Since GT=0/0 represents no variant occurs, the corresponding values of LOINC 69548-6 should be 'absent'.

Prerequisites

  • [v] I am running the latest version
  • [v] I checked the documentation and found no answer
  • [v] I checked to make sure that this issue has not already been filed

Context

  • Package Version: vcf2fhir 0.0.17
  • Operating System: Ubuntu 16.04.6 LTS

Expected Behavior

When GT=0/0, the values of LOINC 69548-6 should be 'absent' (LA9634-2).

Current Behavior

The value of LOINC 69548-6 is fixed. Always shows 'present' whenever the GT values are.

Rohan-cod commented

Hi @Yun-00, thanks for the issue. As per the current translation logic for VCF to FHIR conversion, we exclude the vcf records where FORMAT.GT is in ['0/0', '0|0', '0']. You can find more about the exclusion criteria under the Exclusions section here

Yun-00 commented

Hi @Rohan-cod , Thanks for replying. Maybe i should switch to the current version. Appreciate your great work.

  • 👍1
Rohan-cod commented

Hi @Rohan-cod , Thanks for replying.

No problem. :)

Appreciate your great work.

Thanks @Yun-00. 😇