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diskin-lab-chop / AutoGVP

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Bug: InterVar call with P with PVS1=1, downgrade to LP after autoPVS1 adjustment #100

Closed jungkim2 closed 1 year ago

jungkim2 commented 1 year ago

Provide the command used or report the bug here

For variants that doesn't have ClinVar and taking InterVar call, InterVar is calling Pathogenic, but gets downgraded to Likely_pathogenic in final_call.

Here are some example coordinates

16-3254166-G-T 16-3247248-T-G

What version are you using?

Add error message here (if applicable)

Add Session info

Run sessionInfo() and post the output below

rjcorb commented 1 year ago

@jungkim2 are these variants in any of the test files? I don't seem them.

jungkim2 commented 1 year ago

they are not in the test file. I gave those specific example files to @naqvia

naqvia commented 1 year ago

So for the 16-3247248-T-G it is getting a LP call due to this check in the code: 

ifelse((evidencePVS1 == 1 & evidencePM == 1) |
        (evidencePS == 1 & evidencePM >= 1) |
        (evidencePS == 1 & evidencePP >= 2) |
        (evidencePM >= 3) |
        (evidencePM == 2 & evidencePP >= 2) |
        (evidencePM == 1 & evidencePP >= 4), "Likely_pathogenic",

this is because PVS1=1, PM= 1 and PP=1 from the intervar line: PVS1=1 PS=[0, 0, 0, 0, 0] PM=[0, 1, 0, 0, 0, 0, 0] PP=[0, 0, 1, 0, 0, 0] BA1=0 BS=[0, 0, 0, 0, 0] BP=[0, 0, 0, 0, 0, 0, 0, 0]

This logic is documented in the readme under the Likely pathogenic heading. Can you please comment @jungkim2 and clarify? cc @jharenza

jungkim2 commented 1 year ago

yes, one of them indeed is LP! But other one should be P.

jungkim2 commented 1 year ago

opening new issue with exact variant