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Re: [Vcftools-help] (no subject)
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From: Petr D. <pd...@sa...> - 2013-11-11 08:33:38
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Looks like your VCF headers are broken, but that shouldn't stop
vcf-merge from proceeding. Were the VCF compressed with bgzip and
indexed with tabix? An easy way to check:
This should print the list of chromosomes:
tabix -l file.vcf.gz
This should return a vcf line (set chr,from,to meaningfully):
tabix file.vcf.gz chr:from-to
Petr
On Wed, 2013-11-06 at 07:27 -0800, carol white wrote:
> on one of the vcf.gz file:
>
>
> INFO field at chr1:2372019 .. INFO tag [MQ] not listed in the
> header,INFO tag [DP4] not listed in the header,INFO tag [DP] not
> listed in the header,INFO tag [AF1] not listed in the header,INFO tag
> [VDB] not listed in the header,INFO tag [AC1] not listed in the
> header,INFO tag [INDEL] not listed in the header,INFO tag [PV4] not
> listed in the header,INFO tag [FQ] not listed in the header
> column S1 at chr1:2372019 .. FORMAT tag [PL] not listed in the header
> INFO field at chr1:5313661 .. INFO tag [INDEL] did not expect any
> parameters, got [.]
> INFO field at chr1:6179923 .. INFO tag [INDEL] did not expect any
> parameters, got [.]
> INFO field at chr1:6443619 .. INFO tag [INDEL] did not expect any
> parameters, got [.]
> INFO field at chr1:11047563 .. INFO tag [INDEL] did not expect any
> parameters, got [.]
> INFO field at chr1:16947281 .. INFO tag [INDEL] did not expect any
> parameters, got [.]
>
> INFO field at chr1:19497712 .. INFO tag [INDEL] did not expect any
> parameters, got [.]
>
>
>
>
> and more similar lines for other chr and positions
>
>
> On Wednesday, November 6, 2013 1:42 PM, Laura Clarke <la...@eb...>
> wrote:
>
> Do your other vcf files come out without warnings when running
> vcf-validate
>
>
> Laura
>
> On Wednesday, 6 November 2013, carol white wrote:
> Hi,
> when I installed vcftools, I got many warnings (see below for
> some of them). Then, when I wanted to merge vcf files, I
> wrongly got the following message on the column name whereas
> there is already column name in each vcf file file.
>
>
> Perhaps, I should reinstall vcftools?
> --------------------------------------------------
> vcftools_0.1.11/bin/vcf-merge *.gz > merge.vcf
>
>
>
> Using column name 'S1' for file1.vcf.gz:S1
> Using column name 'S2' for file1.vcf.gz:S2
>
>
> and all other gz file
>
>
> Broken VCF header, no column names?
> at vcftools_0.1.11/perl//Vcf.pm line 177
> Vcf::throw('Vcf4_1=HASH(0x7fdfcb251f98)', 'Broken VCF header,
> no column names?') called at vcftools_0.1.11/perl//Vcf.pm line
> 869
> VcfReader::_read_column_names('Vcf4_1=HASH(0x7fdfcb251f98)')
> called at vcftools_0.1.11/perl//Vcf.pm line 604
> VcfReader::parse_header('Vcf4_1=HASH(0x7fdfcb251f98)') called
> at
> vcftools_0.1.11/bin/vcf-merge line 181
>
> main::init_cols('HASH(0x7fdfcb034ca8)',
> 'Vcf4_1=HASH(0x7fdfcb032c58)') called at
> vcftools_0.1.11/bin/vcf-merge line 277
> main::merge_vcf_files('HASH(0x7fdfcb034ca8)') called at
> vcftools_0.1.11/bin/vcf-merge line 12
>
>
>
>
> ---------------------------------------------------
> make
> g++ -c -O2 -D_FILE_OFFSET_BITS=64 vcftools.cpp -o vcftools.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64 vcftools.cpp > vcftools.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64 bcf_file.cpp -o bcf_file.o
> bcf_file.cpp:474:2: warning: delete called on 'entry' that is
> abstract but has non-virtual destructor
> [-Wdelete-non-virtual-dtor]
> delete e;
> ^
> bcf_file.cpp:541:2: warning: delete called on 'entry' that is
> abstract but has non-virtual destructor
> [-Wdelete-non-virtual-dtor]
> delete e;
> ^
> 2 warnings generated.
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64 bcf_file.cpp > bcf_file.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64 vcf_file.cpp -o vcf_file.o
> vcf_file.cpp:25:13: warning: initialization of pointer of type
> 'gzFile' (aka 'void *') to null from a constant boolean
> expression [-Wbool-conversion]
> gzvcf_in = false;
> ^~~~~
> vcf_file.cpp:315:2: warning: delete called on 'entry' that is
> abstract but has non-virtual destructor
> [-Wdelete-non-virtual-dtor]
> delete e;
> ^
> vcf_file.cpp:394:2: warning: delete called on 'entry' that is
> abstract but has non-virtual destructor
> [-Wdelete-non-virtual-dtor]
> delete e;
> ^
> 3 warnings generated.
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64 vcf_file.cpp > vcf_file.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64 variant_file.cpp -o
> variant_file.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64 variant_file.cpp >
> variant_file.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64 bcf_entry.cpp -o
> bcf_entry.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64 bcf_entry.cpp >
> bcf_entry.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64 vcf_entry.cpp -o
> vcf_entry.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64 vcf_entry.cpp >
> vcf_entry.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64 entry.cpp -o entry.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64 entry.cpp > entry.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64 entry_setters.cpp -o
> entry_setters.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64 entry_setters.cpp >
> entry_setters.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64 entry_getters.cpp -o
> entry_getters.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64 entry_getters.cpp >
> entry_getters.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64 vcf_entry_setters.cpp -o
> vcf_entry_setters.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64 vcf_entry_setters.cpp >
> vcf_entry_setters.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64 bcf_entry_setters.cpp -o
> bcf_entry_setters.o
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64 bcf_entry_setters.cpp >
> bcf_entry_setters.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64 variant_file_filters.cpp -o
> variant_file_filters.o
> variant_file_filters.cpp:35:2: warning: delete called on
> 'entry' that is abstract but has non-virtual destructor
> [-Wdelete-non-virtual-dtor]
> delete e;
> ^
> variant_file_filters.cpp:1341:2: warning: delete called on
> 'entry' that is abstract but has non-virtual destructor
> [-Wdelete-non-virtual-dtor]
> delete e;
> ^
> 18 warnings generated.
> g++ -MM -O2 -D_FILE_OFFSET_BITS=64 variant_file_filters.cpp >
> variant_file_filters.d
> g++ -c -O2 -D_FILE_OFFSET_BITS=64 variant_file_output.cpp -o
> variant_file_output.o
> variant_file_output.cpp:148:2: warning: delete called on
> 'entry' that is abstract but has non-virtual destructor
> [-Wdelete-non-virtual-dtor]
> delete e;
> ^
> variant_file_output.cpp:278:2: warning: delete called on
> 'entry' that is abstract but has non-virtual destructor
> [-Wdelete-non-virtual-dtor]
> delete e;
> ^
> v
>
>
>
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