Question: bcftools merge failed: incorrect number of PL fields
1
gravatar for QVINTVS_FABIVS_MAXIMVS
15 months ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.2k 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 • 1.2k views
ADD COMMENTlink written 15 months ago by QVINTVS_FABIVS_MAXIMVS2.2k
2
gravatar for Kevin Blighe
15 months ago by
Kevin Blighe41k
Guy's Hospital, London
Kevin Blighe41k 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 15 months ago by Kevin Blighe41k
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 15 months ago • written 15 months ago by Kevin Blighe41k

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 15 months ago by QVINTVS_FABIVS_MAXIMVS2.2k
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 15 months ago by Kevin Blighe41k

Ahh I see. Thanks for the help

ADD REPLYlink written 15 months ago by QVINTVS_FABIVS_MAXIMVS2.2k
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