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?
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.
Deniz, If the response from rlong is helpful, please vote it up and consider "accepting" it as well. This is what makes BioStar so good. If you have another question to pose, please do so as a separate entry.
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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.