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Plugin +mendelian2 reports missing samples incorrectly #2242

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allytrope opened this issue Aug 2, 2024 · 2 comments
Closed

Plugin +mendelian2 reports missing samples incorrectly #2242

allytrope opened this issue Aug 2, 2024 · 2 comments

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@allytrope
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Given a VCF containing samples 101, 102, and 103, the following seems to works:
bcftools +mendelian2 test.vcf.gz -p 101,102,103

However, if I run the command instead to include an arbitrary sample for the child not in the VCF like so:
bcftools +mendelian2 test.vcf.gz -p 0,102,103, then it actually reports that the mother is missing: The sample is not present: 103.

In reverse, if the mother is actually the missing one, it instead reports that the child id is missing.

The missing father does work as expected though,

@pd3 pd3 closed this as completed in a3993dd Aug 6, 2024
@pd3
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pd3 commented Aug 6, 2024

Thank you for reporting the bug, it is fixed now. Note the problem was only the error message, the program was assigning the family members correctly in the calculation

@allytrope
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Great! Thanks for fixing it!

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