Re: [Vcftools-help] vcf-merge error

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Thank you very much,

Maybe is because my VCF versions. one of my files is VCFv4.0 and the other
VCFv4.2. Can I convert these files from one version to the other? If this
is not the problem I guess that I am going to remove the tags as you
suggest.

Best Wishes,

Eric

2016-10-13 14:25 GMT-05:00 Petr Danecek <pd...@sa...>:

> Both programs, bcftools merge and vcf-merge, expect valid VCFs on input.
> If you don't care about PL and GQ tags, you can remove them using
> `bcftools annotate -x` and merge afterwards.
>
> On Thu, 2016-10-13 at 13:14 -0500, Eric González wrote:
> > 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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> >         > _______________________________________________
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> >         https://lists.sourceforge.net/lists/listinfo/vcftools-help
> >
> >
> >
> >
> >         --
> >          The Wellcome Trust Sanger Institute is operated by Genome
> >         Research
> >          Limited, a charity registered in England with number 1021457
> >         and a
> >          company registered in England with number 2742969, whose
> >         registered
> >          office is 215 Euston Road, London, NW1 2BE.
> >
> >
> >
> > --
> > Eric
>
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>

-- 
Eric