bcftools filter -e doesn't work for gVCF REF field

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

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bcftools filter -e doesn't work for gVCF REF field #2005

Closed PlatonB closed 1 year ago

PlatonB commented 1 year ago

Ubuntu 20.04.1
bcftools 1.17 (bioconda)
htslib 1.18 (bioconda)

My goal is to filter out such meaningless gVCF lines:

chr1    1       .       N       .       .       .       .       GT:DP:RGQ       ./.     ./.     ./.:0:0 ./.     ./.:0:0 ./.     ./.:0:0 ./.     ./.:0:0 ./.     ./.:0:0

But such a seemingly trivial command doesn't work:

bcftools filter -e REF="N" coh_chr{2}.g.vcf.gz

Error: cannot use arithmetic operators to compare strings and numbers

pd3 commented 1 year ago

This is supported in the latest github version, please check how to install from source code here http://samtools.github.io/bcftools/howtos/install.html