Question: Vcftools: Vcf-Isec Error The Column Names Do Not Match.
3
gravatar for Deniz
7.3 years ago by
Deniz200
Deniz200 wrote:

I have vcf 4.1 format. It was saying first the VCF appears to be invalid. According to VCF specification, the fields "Number=-1" should be "Number=." in VCFv4.0.

I edited my vcf file. but this time giving the following error:

[dincera@hpcc01 test]$ /home/dincera/vcftools_0.1.6/perl/vcf-isec -o -n +11 1.vcf.gz 2.vcf.gz 3.vcf.gz 4.vcf.gz 5.vcf.gz 6.vcf.gz 7.vcf.gz 8.vcf.gz 9.vcf.gz 10.vcf.gz 11.vcf.gz| /home/X/tabix-0.2.5/bgzip -c > overlap.vcf.gz

Warning: The column names do not match (e.g. NA00001):
NA00001
1185N
 at /home/X/vcftools_0.1.6/perl/vcf-isec line 21
    main::error('Warning: The column names do not match (e.g. NA00001):\x{a}NA0000...') called at /home/X/vcftools_0.1.6/perl/vcf-isec line 87
    main::__ANON__('Warning: The column names do not match (e.g. NA00001):\x{a}NA0000...') called at /home/X/vcftools_0.1.6/perl/vcf-isec line 165
    main::check_columns('HASH(0x14bd9e8)', 'ARRAY(0x14840a8)') called at /home/X/vcftools_0.1.6/perl/vcf-isec line 234
    main::vcf_isec('HASH(0x14bd9e8)') called at /home/X/vcftools_0.1.6/perl/vcf-isec line 12

What should I do?

vcf vcftools • 4.9k views
ADD COMMENTlink modified 7.3 years ago by pd3340 • written 7.3 years ago by Deniz200

Hi @Deniz. In respect for the users of this forum, which are eager to help you, please take some time to post questions in an easier to understand format.

ADD REPLYlink written 7.3 years ago by Eric Normandeau10k
2
gravatar for Rlong
7.3 years ago by
Rlong340
US
Rlong340 wrote:

It looks like this tool is requiring that you use vcfs from the same sample. Since the column name of the per-sample data in VCF is the name of the sample, it is telling you that these don't match and refusing to proceed. If you include the -f option to force it, it should proceed as requested.

ADD COMMENTlink written 7.3 years ago by Rlong340
0
gravatar for pd3
7.2 years ago by
pd3340
pd3340 wrote:

Use the -f option of vcf-isec. For also other options, type vcf-isec -h

ADD COMMENTlink written 7.2 years ago by pd3340
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