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Bcftools query does not recognize arithmetic functions #2349

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smlchen opened this issue Dec 31, 2024 · 0 comments
Open

Bcftools query does not recognize arithmetic functions #2349

smlchen opened this issue Dec 31, 2024 · 0 comments

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@smlchen
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smlchen commented Dec 31, 2024

> bcftools --version
bcftools 1.21
Using htslib 1.21
Copyright (C) 2024 Genome Research Ltd.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
> bcftools query -f "%CHROM %POS %SUM(FORMAT/AD)" test.vcf.gz
Error: no such tag defined in the VCF header: INFO/SUM

According to the documentation for bcftools query, as quoted below,

Format:
%CHROM The CHROM column (similarly also other columns: POS, ID, REF, ALT, QUAL, FILTER)
%END End position of the REF allele
%END0 End position of the REF allele in 0-based coordinates
%FIRST_ALT Alias for %ALT{0}
%FORMAT Prints all FORMAT fields or a subset of samples with -s or -S
%GT Genotype (e.g. 0/1)
%FUNCTION Functions supported by the -i/-e filtering expressions (e.g. "[ %sSUM(FMT/AD)] %SUM(FMT/AD) %SUM(INFO/AD)")

my command should work, but it returns an error. What am I missing?

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