search

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
http://samtools.github.io/bcftools/
Other
681 stars 240 forks source link

Consensus of ALTs only without genotypes in file #2315

Open schorlton-bugseq opened 2 weeks ago

schorlton-bugseq commented 2 weeks ago

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 commented 1 week ago

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 commented 1 week ago

Awesome. Thank you :smile: