bcftools merge failed: incorrect number of PL fields

Question

[QVINTVS_FABIVS_MAXIMVS]

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?

Answer 1

[Kevin Blighe]

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

[Kevin Blighe]

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.

[QVINTVS_FABIVS_MAXIMVS]

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?

[Kevin Blighe]

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.

[QVINTVS_FABIVS_MAXIMVS]

Ahh I see. Thanks for the help