search

diskin-lab-chop / AutoGVP

19 stars 3 forks source link

Bug: ClinVar 1NR not getting consensus calls #116

Closed jungkim2 closed 1 year ago

jungkim2 commented 1 year ago

Provide the command used or report the bug here

With most recent version ClinVar 1NR calls are not getting correct consensus calls.

If ClinVar is 1NR,

  1. If there is majority, majority calls should be taken
  2. If tie, most recent needs to be taken

Some example vcf_id not getting the correct calls

1-11022268-G-A currently getting VUS, expect LP

1-11046609-T-C currently getting VUS, expected LP

1-43338669-G-A currently getting LB, expected B

10-133366990-G-A currently getting VUS, expect LP

What version are you using?

issue11 branch

Add error message here (if applicable)

Add Session info

Run sessionInfo() and post the output below

jharenza commented 1 year ago

issue11 branch

Hi - to clarify, when you run this from the main branch, do you still see this issue?

jungkim2 commented 1 year ago

I have not tested on the main branch. But will test out the branch issue116 first

jungkim2 commented 1 year ago

issue resolved