vcftools merge: Incorrect number of F1R2 fields (2) at chr12:29486505, cannot merge.

Question

[Shicheng Guo]

Hi All,

I want to merge 38 vcf files with bcftools merge:

bcftools merge --force-samples -l input.txt -Oz -o LungBrain.vcf.gz

However, bcftools report error:

Incorrect number of F1R2 fields (2) at chr12:29486505, cannot merge.

I checked this variant and found:

chr12   29486505    .   CAG     C,CTAG  16.87   .  GT      0/0     0/0     ./.     0/2

Any suggestion?

Thanks.

[WouterDeCoster]

I would suggest switching to bcftools. That may or may not solve your issue, but it is the recommended tool to manipulate vcf files nowadays.

[Shicheng Guo]

I just forcely removed this variant. I know it is not best solution to do that but it do work. after I remove this variant, the whole pipeline works.

[WouterDeCoster]

After having another look at this, the "1" allele is missing from this. You have a multivariate position, but only a 0 and a 2 allele.

[Ram]

One should always bcftools norm a VCF with the reference fasta before further manipulating the file with bcftools, as a lot of things can go (semantically) wrong with operations such as merge or concat when multi-allelic variants are involved.