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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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bcftools 1.19 annotate not working with "." and "+" modifiers for adding TAG fields #2038

Closed epsalazarf closed 9 months ago

epsalazarf commented 9 months ago

Hi,

So I recently updated bcftools to the latest version (1.19) and found out that my annotations scripts are not working as intended anymore. If I try the following command:

bcftools annotate -a ref.vcf.gz -c .+ID input.vcf.gz

I get the message: The tag ".+ID" is not defined in ref.vcf, taking the modifiers ("." to replace missing IDs, "+" to not replace present IDs) literally as a field name.

But according to the bcftools annotate documentation, this is the correct usage and the same command works perfectly in the previous 1.18 version.

Has this behavior been modified (for which I couldn't find documentation) or is it a bug?

pd3 commented 9 months ago

There is no such release as 1.19. Maybe you are running 1.9 by mistake?