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bcftools annotate labels transferred FILTER column as single value "Number=1" in header #2335

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toddajohnson opened this issue Dec 13, 2024 · 0 comments

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@toddajohnson
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I annotated a VCF with another VCF of TOMMO allele frequency data, including updating the FILTER field and several INFO TAGs.
VCF sites have FILTER as ".", "PASS", or one or more semicolon delimited FILTER flags.
I then ran "bcftools annotate -c INFO/TOMMO_FILTER:=FILTER -Ov -o test_anno.vcf test.vcf" to add an INFO field for the FILTER field. Semicolons in the FILTER field were correctly replaced with commas in instantiating the TOMMO_FILTER field, but the header line was:
##INFO=<ID=TOMMO_FILTER,Number=1,Type=String,Description="Transferred FILTER column">

So, instead of "Number=." to record that the tag can have any number of values, it contained "Number=1". I don't know if that impacts bcftools parsing of that field in dowstream analyses, but in using R VariantAnnotation package, it recognizes that TOMMO_FILTER has only a single value, and thus only parses the first value in the TOMMO_FILTER.

Is the assignment of "Number=1" expected behavior?

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