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diskin-lab-chop / AutoGVP

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Bug: autoPVS1 unmet but still getting P/LP #101

Closed jungkim2 closed 1 year ago

jungkim2 commented 1 year ago

Provide the command used or report the bug here

Variants that have no ClinVar call, and the reasoning for call is InterVar InterVar calls it Pathogenic, and final output is Likely_pathogenic

InterVar: Pathogenic 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]

However, when autoPVS1 file is checked, it has NF4, unmet Therefore, in this particular case, PVS1=1 should not be counted, therefore total counts would be PM=1, PP=1 VUS.

7-93131357-C-A 7-93135631-G-T

What version are you using?

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rjcorb commented 1 year ago

@jungkim2 I cannot locate these variants in any of the test files

jungkim2 commented 1 year ago

they are not. These were found when I was testing different set of files that I wanted to test.

naqvia commented 1 year ago

Problem and issue resolved. AutoPVS1 related statements modified, tested and merged.