Sorry, I have been trying to work this out desparately all day. Biostars couldn't find any answer so I am cross posting here.

I am trying to get both the left and right reference genome using a sample name in phase VCF file.

This works:

bcftools consensus -f lyrata_chr01-short.fasta phasedVCF-short.vcf.gz -s ms01e -H 1 > ms01e-left.fa

When I am trying to make the new Ref Sequence by imputing genotype from the right haplotype, this doesn't work.

bcftools consensus -f lyrata_chr01-short.fasta phasedVCF-short.vcf.gz -s ms01e -H 2 > ms01e-right.fa
Broken VCF, too few alts at 1:141

What is the issue ?

Here is my VCF data:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  MA605   MA611   MA622   MA625   MA629   Ncm8    Sp154   Sp164   Sp21    Sp3 Sp76    SpNor33 ms01e   ms02g   ms03g   ms04h
1   141 .   C   T   .   .   .   GT:PG:PG_al:PI  .   .   .   0|1:0|1:C|T:10763   .   .   .   .   .   .   .   .   .   .   .   .
1   3697    .   T   C   .   .   .   GT:PG:PG_al:PI  .   0|0:0|0:T|T:11398   .   0|1:0|1:T|C:8039    0|1:0|1:T|C:8202    0|1:0|1:T|C:4616    0|1:0|1:T|C:3938    .   0|1:0|1:T|C:5102    .   .   0|1:0|1:T|C:17340   1|0:1|0:C|T:1   .   .   .

The GT field is empty at POS 141 for SAMPLE ms01e, but in that situation it should by default pick a REF allele. Isn't it? And, it only is the problem when doing -H 2 not -H 1.

Update: I have been trying to fix this issue by playing with -i and -e using the BCFtools manual. But, still cannot find the fix.

  • $\begingroup$ I don't know much about VCF but the first row seems to have less fields than the second. Is this normal/accepted format ? Also did you try the latest version (as per ) ? $\endgroup$
    – llrs
    May 18, 2018 at 8:43


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