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EBIvariation / vcf-validator

Validation suite for Variant Call Format (VCF) files, implemented using C++11
Apache License 2.0
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Is underscore not allowed to be used? #207

Closed htchihiro closed 3 years ago

htchihiro commented 3 years ago

Hi,

When validating my vcf file using vcf_validator, I am getting an error message.

Error message: According to the VCF specification, the input file is not valid Error: Format is not a colon-separated list of alphanumeric strings. This occurs 34 time(s), first time in line 41.

line 40 - 42 in my vcf file

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12891

demo20 1 . T . . LowGQX END=899;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP .:.:0:0:0 demo20 900 . G . . LowGQX;LowDepth END=906;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:5:2:0:2

I removed underscore"_" from BLOCKAVG_min30p3a and MIN_DP. My vcf file passed the validation.

If we can't use underscore, we hope it can. This is because many VCF-creating tools include underscores. Could you please check it?

tcezard commented 3 years ago

Hi @htchihiro Could you specify which version of the VCF format you are using ? underscores were not allowed in version 4.2 (see section 1.4.2) but are now allowed in version 4.3 (section 1.6.2)

Does this explain your issue ?

htchihiro commented 3 years ago

Thanks for the answer and the important information.

I used vcf version 4.1. I will update the vcf version. I understand that this validator checks the vcf version and changes the validation rules according to that version, is that correct?

tcezard commented 3 years ago

Yes this is correct.