Question: bcftools merge failed: incorrect number of PL fields
1
gravatar for QVINTVS_FABIVS_MAXIMVS
2.2 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.4k wrote:

I'm using bcftools merge and I get this error

Incorrect number of PL fields (3) at chr1:10240, cannot merge.

I believe this is due to different versions of bcftools/GATK. However, I do not care about the PL fields. Is there a way for me to skip this error (make it a warning) or do I have to reformat the VCFs?

bcftools merge vcf • 1.8k views
ADD COMMENTlink written 2.2 years ago by QVINTVS_FABIVS_MAXIMVS2.4k
2
gravatar for Kevin Blighe
2.2 years ago by
Kevin Blighe56k
Kevin Blighe56k wrote:

I would just normalise the BCFs or VCFs before attempting to merge them. Take a quick look at the sequence of commands here: bcftools consensus error

ADD COMMENTlink written 2.2 years ago by Kevin Blighe56k
1

I believe this is due to different versions of bcftools/GATK

Yes, it is: https://github.com/samtools/bcftools/issues/110

These things happen in bioinformatics.

It should not be an issue to re-analyse your data using updated versions. Also, I strongly encourage you to normalise your BCFs/VCFs, as to which I have alluded - this will save you from other types of headaches.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Kevin Blighe56k

Thanks, I've used bcftools norm to left-align and to split multiallelic sites into biallelic sites (for plink). I solved the issue by removing the PL entries. How would bcftools norm work in this situation of differing versions?

ADD REPLYlink written 2.2 years ago by QVINTVS_FABIVS_MAXIMVS2.4k
1

It was just a way of making sure that other issues unrelated to the PL were not the cause. Sometimes error messages are hopelessly unhelpful.

glad that you got it sorted.

ADD REPLYlink written 2.2 years ago by Kevin Blighe56k

Ahh I see. Thanks for the help

ADD REPLYlink written 2.2 years ago by QVINTVS_FABIVS_MAXIMVS2.4k
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