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

[Petr D. <pd...@sa...>]

The program is doing the correct thing, please check the VCF
specification
http://samtools.github.io/hts-specs/VCFv4.3.pdf

If your VCF is broken and you don't care about the PL fields, replace
the Number=G definition in the header with Number=. 

Petr



On Tue, 2018-02-27 at 13:17 -0800, Sarah Signor wrote:
> 
> 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
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