Re: [Vcftools-help] (no subject)

[carol w. <wh...@ya...>]

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