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bcftools annotate does not add new field to INFO #1733

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TedBrookings opened this issue Jun 9, 2022 · 1 comment
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bcftools annotate does not add new field to INFO #1733

TedBrookings opened this issue Jun 9, 2022 · 1 comment

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@TedBrookings
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I've run into what looks like a regression introduced in release 1.14 (our scripts work for 1.13 and earlier, and fail for 1.14 and later). But possibly the method of invoking bcftools annotate has changed?
I'm attempting to use a tab-delimited annotation file to add a field to INFO. The original task uses more of annotate's capabilities, but I've made a stripped down small data set and simple command (e.g. the supplied VCF already has the new field in the header). I attached a zip file with the VCF, annotations file, and its index. This is the command:

bcftools annotate -a evidence_annotations.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE test.vcf.gz

Versions 1.13 and earlier add EVIDENCE to INFO, and versions 1.14 and later don't.
test_files.tar.gz

@pd3
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pd3 commented Jun 13, 2022

This is now fixed, thank you for the bug report and for the test case. Please let me know if you spot anything odd.

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