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Problem with REF/ALT normalization in VCF #99

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holtgrewe opened this issue Oct 11, 2023 · 0 comments · Fixed by #100
Closed

Problem with REF/ALT normalization in VCF #99

holtgrewe opened this issue Oct 11, 2023 · 0 comments · Fixed by #100
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bug Something isn't working

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@holtgrewe
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Describe the bug
For input as below

19 5687506 . GC GT

The first base should be trimmed. The annotator does this but does not update the position leading to a wrong location.

19 5687506 . C T

The correct output is

19 5687507 . C T

Such input is probably rare, affects multiallelic sites, and did not occur previously as our installation does this normalization with bcftools norm.
@holtgrewe holtgrewe added the bug Something isn't working label Oct 11, 2023
holtgrewe added a commit that referenced this issue Oct 11, 2023
@holtgrewe
Fixing problem with left-trimming variants (#99)
15c3654
@holtgrewe holtgrewe linked a pull request Oct 11, 2023 that will close this issue
Fixing problem with left-trimming variants (#99) #100
Merged
holtgrewe added a commit that referenced this issue Oct 11, 2023
@holtgrewe
Fixing problem with left-trimming variants (#99)
2a15ca4 
Closes: #99
Related-Issue: #99
Projected-Results-Impact: medium
holtgrewe added a commit that referenced this issue Oct 11, 2023
@holtgrewe
Fixing problem with left-trimming variants (#99)
6ae64a1 
Closes: #99
Related-Issue: #99
Projected-Results-Impact: require-revalidation
holtgrewe added a commit that referenced this issue Oct 11, 2023
@holtgrewe
Fixing problem with left-trimming variants (#99)
e506abd 
Closes: #99
Related-Issue: #99
Projected-Results-Impact: require-revalidation
holtgrewe added a commit that referenced this issue Oct 11, 2023
@holtgrewe
Fixing problem with left-trimming variants (#99)
5a46f9f 
Closes: #99
Related-Issue: #99
Projected-Results-Impact: require-revalidation
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Fixing problem with left-trimming variants (#99) varfish-org/varfish-annotator
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