Re: [Vcftools-help] vcf-merge error

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

Hi Eric,

the error messages indicate that the VCF files on input have incorrect
number of values for the PL field at the position 1:201777216. Please
check vcf-validator and VCF specification
http://samtools.github.io/hts-specs/VCFv4.3.pdf

By the way, the perl side vcf-tools has been made obsolete by the new
(and much faster) bcftools
http://samtools.github.io/bcftools/

Best wishes,
Petr

On Wed, 2016-10-12 at 16:59 -0500, Eric González wrote:
> Hi
> 
> I am using vcf-merge to join to vcf files, one contain the data of 56
> individuals and the other of only one. One of my files have 524754
> SNPs and the other 105878 however when I join them I obtain just a few
> SNPs ~50000 SNPs and I obtain the next message error:
> 
> Wrong number of values in LANMLR17B064:250550525/PL at 1:201777216 ..
> nAlleles=4, nValues=3.
> Expected 10 values for diploid genotypes or 4 for haploid genotypes.
> 
>  at /LUSTRE/storage/data/software/vcftools/lib/perl5/site_perl/Vcf.pm
> line 172, <$__ANONIO__> line 9640.
>     Vcf::throw(Vcf4_0=HASH(0x7b11a8), "Wrong number of values in
> LANMLR17B064:250550525/PL at 1:2017"...) called
> at /LUSTRE/storage/data/software/vcftools/lib/perl5/site_perl/Vcf.pm
> line 1767
>     VcfReader::parse_AGtags(Vcf4_0=HASH(0x7b11a8), HASH(0xb37ed0))
> called at /LUSTRE/storage/data/software/vcftools/bin/vcf-merge line
> 464
>     main::merge_vcf_files(HASH(0xa4e960)) called
> at /LUSTRE/storage/data/software/vcftools/bin/vcf-merge line 12
> 
> when I run vcf-validate in one of my files I get the next:
> 
> vcf-validator -u  PTxB73BC1S5RIL_0.1_0.9_56ind_V3_sorted.vcf.gz
> Leading or trailing space in attr_key-attr_value pairs is discouraged:
>     [Population] [  ]
> 
> SAMPLE=<ID=LANMLR17B002:250550514,Barcode=CTCGA,BarcodeWell=A04,Col=4,DNASample=LANMLR17B002,DNA_Plate=PTXB73_RIL,Enzyme=ApeKI,Flowcell=C81KJANXX,Flowcell_Lane=C81KJANXX_6,FullSampleName=LANMLR17B002:C81KJANXX:6:250550514,Genus=Zea,Lane=6,LibraryPlate=PTXB73_RIL,LibraryPlateID=450024469,LibraryPrepID=250550514,Population=  ,Row=A,SampleDNA_Well=A04,Species=mays,Status=private>
> 1:1785738 .. Could not parse the allele(s) [N], first base does not
> match the reference.
> 2:17275732 .. REF allele listed in the ALT field??
> 
> 
> ------------------------
> Summary:
>     3337 errors total 
> 
>     3168    ..    1:1785738 .. Could not parse the allele(s) [N],
> first base does not match the reference.
>     55    ..    Leading or trailing space in attr_key-attr_value pairs
> is discouraged:
>     55    ..     [Population] [ ]
>     55    ..
>  SAMPLE=<ID=LANMLR17B002:250550514,Barcode=CTCGA,BarcodeWell=A04,Col=4,DNASample=LANMLR17B002,DNA_Plate=PTXB73_RIL,Enzyme=ApeKI,Flowcell=C81KJANXX,Flowcell_Lane=C81KJANXX_6,FullSampleName=LANMLR17B002:C81KJANXX:6:250550514,Genus=Zea,Lane=6,LibraryPlate=PTXB73_RIL,LibraryPlateID=450024469,LibraryPrepID=250550514,Population= ,Row=A,SampleDNA_Well=A04,Species=mays,Status=private>
>     4    ..    2:17275732 .. REF allele listed in the ALT field??
> 
> and in the other:
> 
> vcf-validator -u  PTxB73F1_filtrado_sorted.vcf_bgzip.gz        
> INFO field at 1:57749972 .. Could not validate the float [NaN]
> 
> 
> ------------------------
> Summary:
>     29 errors total 
> 
>     29    ..    INFO field at 1:57749972 .. Could not validate the
> float [NaN]
> 
> vcf-validator -u  PTxB73F1_filtrado_sorted.vcf_bgzip.gz        
> INFO field at 1:57749972 .. Could not validate the float [NaN]
> 
> 
> ------------------------
> Summary:
>     29 errors total 
> 
>     29    ..    INFO field at 1:57749972 .. Could not validate the
> float [NaN]
> 
> Could anyone tell me what is happening?
> 
> Best Wishes,
> 
> 
> -- 
> Eric
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