Consensus of ALTs only without genotypes in file

[schorlton-bugseq]

I have a VCF without genotypes or FORMAT column. The ALT field can have multiple alleles. Example:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
test	1478	.	C	T,A	3232	PASS	DP=36715;AF=0.120142;SB=132;DP4=103,159,2782,1629

Is it possible to apply all ALT alleles but not the REF allele to a consensus with IUPAC? I tried bcftools consensus -f ref.fna --iupac-codes test.vcf.gz but I'm getting an H at this position instead of W. I also tried --haplotype but it did not appear to impact behaviour as missing the sample info.

Thanks!

[pd3]

Currently not. An easy workaround would be to add the FORMAT/GT column referring to the alternate alleles and run with -H I. I'll mark it as enhancement

[schorlton-bugseq]

Awesome. Thank you :smile: