Vcftools: Vcf-Isec Error The Column Names Do Not Match.

Question

[Deniz]

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?

[Eric Normandeau]

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.

Answer 1

[Rlong]

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.

Answer 2

[pd3]

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