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vcf-expression-annotator updates - #92

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chrisamiller merged 1 commit into
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chrisamiller:expression
Jul 7, 2026
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chrisamiller merged 1 commit into
griffithlab:masterfrom
chrisamiller:expression

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  1. updates the docs to reflect that it writes to the FORMAT field, not INFO

  2. Right now, it's impossible to annotate two different samples in the same VCF with GX tags, as the tool will die when it encounters GX in the header. This fixes it with the following flags:

--force allows the tool to proceed, even if it sees an existing GX flag
--overwrite allows the tool to overwrite existing GX values. By default, it will only overwrite blank or absent values (same goes for the TX field on both of these). This is "safer" against unintended overwriting.

  1. adds tests of both of these params

  2. updates docs with both of these params

Closes #82

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+1

@chrisamiller
chrisamiller merged commit c816f73 into griffithlab:master Jul 7, 2026
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Allow vcf-expression-annotator to work on multiple samples or work on a VCF that has previously been annotated

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