Re: [Vcftools-help] vcf-merge error

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Hi

Using bcftools I have the next error:

Could not parse the header line:
"##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>"

This is because the bcftools version right? I am using bcftools/1.2

I also have the next errors:

[W::bcf_hdr_check_sanity] PL should be declared as Number=G
Warning: trying to combine "GQ" tag definitions of different types
Warning: trying to combine "PL" tag definitions of different lengths
Warning: trying to combine "PL" tag definitions of different types

I call the snps of my two files using different programs one using TASSEL
and the other using GATK. Can I convert the INFO fileds of these files? or
what do you think could be the solution to this? call the SNPs using the
same software?

2016-10-13 2:41 GMT-05:00 Petr Danecek <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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-- 
Eric