Consensus of ALTs only without genotypes in file

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
40/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Reproduce the behavior with ref.fna, test.vcf.gz, and the shown bcftools consensus command. Read the consensus handling for --iupac-codes and records without FORMAT or genotypes, then determine whether multiple ALT alleles can produce W while excluding REF. Done means the requested ALT-only consensus behavior is implemented and verified.

Written by the indexing model from the issue text.

Description

enhancement

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!

Dominant language
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