[Vcftools-help] VCF validator

[Neeba D. <nee...@gm...>]

Hi guys,

I extracted a single genome from 1000 genome vcf file

and validate it with VCF -validator

Some files are validate properly  and some files  shows error

nsebastian@ip-10-0-14-69:/store/data$ vcf-validator HG00097.vcf
FIXME: parse_header must be called before next_data_hash.

 at /store/software/vcftools_0.1.6/perl/Vcf.pm line 169
        Vcf::throw('Vcf4_0=HASH(0x18141b8)', 'FIXME: parse_header must be
called before next_data_hash.\x{a}') called at
/store/software/vcftools_0.1.6/perl/Vcf.pm line 484
        VcfReader::next_data_hash('Vcf4_0=HASH(0x18141b8)') called at
/store/software/vcftools_0.1.6/perl/Vcf.pm line 2045
        VcfReader::run_validation('Vcf4_0=HASH(0x18141b8)') called at
/store/software/vcftools_0.1.6/bin/vcf-validator line 60
        main::do_validation('HASH(0x147cd48)') called at
/store/software/vcftools_0.1.6/bin/vcf-validator line 14


What is this error? Also this means its not avalid vcf file. Or we can
negelect this error

Also I tested with a simple file

It shows error

nsebastian@ip-10-0-14-69:/store/data$ vcf-validator out1.vcf
2:160 .. Could not parse the allele(s) [C], first base does not match the
reference.

Please share waht propertes are the function vcf-validator validating


Thanks
Neeba