[Vcftools-help] Format tag [PL] expected different number of values

[Sarah S. <ss...@us...>]

Hello all,

I am using a vcf file that I did not produce, it was provided as
supplementary material from a manuscript. It is old, produced most likely
with versions of all of this software from around 2012.

I am trying to merge the VCFs as the authors provided them split by
genotype, and I keep getting this error:

'Could not determine the ploidy (nals=1, nvals=3).

If using vcftools version 1.12, and this error:

Use of uninitialized value within @gtypes in hash element at
/Users/sarah/Downloads/vcftools_0.1.10/perl//Vcf.pm line 1753, <__ANONIO__>
line 287.

If using 1.10.

And indeed, vcf validator has the following to say:

FORMAT tag [PL] expected different number of values (expected 1, found 3)


The most recent version of vcftools errors as follows:


Wrong number of values in 23/PL at YHet:102954 .. nAlleles=1, nValues=3.

Expected 1 values for diploid genotypes or 1 for haploid genotypes.



I"ll admit I was using legacy versions of VCFtools to try and avoid any
difficulties relating to changes in file format, but clearly its not
working. Did VCF files used to have a different number of PL fields? Is
there something deeply wrong with this VCF file? Is this some kind of bug
with VCFtools?

I realize I might be asking a question about VCF files in general rather
than VCFtools in particular, but any insight would really be appreciated.

Thanks, Sarah