bcftools consensus always output "Applied 0 variants" and does not change the reference sequence.

[shiro-kur]

Hello. There is something wrong with "bcftools consensus" recently.

Finally I tried to convert some nucleotides in simple files below, as examples.
Can you reproduce these errors? and How can we solve the problem.

$ bcftools --version
bcftools 1.20
Using htslib 1.20
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.

$ zcat ex.vcf.gz
##fileformat=VCFv4.1
##contig=<ID=chr1,length=4>
#CHROM POS ID REF ALT QUAL FILTER INFO
chr1 1 . A T . . .

$ cat ex.fa

chr1
ATGC

$ bcftools consensus -f ex.fa ./ex.vcf.gz -o ./ex2.fa
Applied 0 variants

(bcftools) [shiro2@rc026 ""]$ cat ex2.fa

chr1
ATGC

The vcf files was compressed and indexed as followings.
$ bgzip ex.vcf
$ bcftools index ex.vcf.gz

[pd3]

The program had a usage bug, it required -s - even when no samples were present. This is now fixed. Moreover, a message is printed to indicate whether FORMAT/GT or REF,ALT is being applied.

Thanks for reporting the problem