Question: vcftools merge: Incorrect number of F1R2 fields (2) at chr12:29486505, cannot merge.
0
gravatar for Shicheng Guo
17 months ago by
Shicheng Guo8.5k
Shicheng Guo8.5k wrote:

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.

snp vcftools f1r2 merge • 388 views
ADD COMMENTlink written 17 months ago by Shicheng Guo8.5k
2

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.

ADD REPLYlink written 17 months ago by WouterDeCoster44k

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.

ADD REPLYlink written 17 months ago by Shicheng Guo8.5k
2

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.

ADD REPLYlink written 17 months ago by WouterDeCoster44k

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.

ADD REPLYlink modified 17 months ago • written 17 months ago by _r_am31k
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