Vcf Validator From Vcf Tools

Question

[Maria]

How to validate VCF file

I validate with vcf tools vcf - validator

Some files it validate with out any error message but most ofthe vcf files shows some error message

Any option to use with VCF - validator

Also please share that the mandatory fields and faetures of a vcf file

[Sean Davis]

What are the error messages? How were the VCF files created?

Answer 1

[Dan]

Options for vcf-validator:

./vcftools/bin/vcf-validator -h

Usage: vcf-validator [OPTIONS] file.vcf.gz
Options:
   -d, --duplicates                 Warn about duplicate positions.
   -u, --unique-messages            Output all messages only once.
   -h, -?, --help                   This help message.

Answer 2

[Sean Davis]

Here are the specifications for VCF4.0 and the draft for VCF4.1.