vcf_validator error message

samarth51 commented 3 years ago

Hi Team,

When validating my vcf files using vcf_validator using linux version, I am getting an error message.

ERROR MESSAGE:

According to the VCF specification, the input file is not valid Error: FORMAT metadata Number is not a number, A, G or dot. This occurs 1 time(s), first time in line 54.

My vcf format is :fileformat=VCFv4.1 Command used: vcf_validator_linux -i input.vcf -l error

Can you please check the error and let me know how to proceed with this? Please let me know in case more data information is required.

Many Thanks

jmmut commented 3 years ago

can you show us your line number 54? It seems you defined a FORMAT field with an invalid Number.

samarth51 commented 3 years ago

fileformat=VCFv4.1

samtoolsVersion=1.2

reference=hg19.fa

contig=

INFO=

FORMAT=

FILTER=

##FORMAT=

FORMAT=

INFO=

FORMAT=

INFO=

FILTER=

INFO=

FILTER=

LINE54 ##FORMAT=

Though we have not made any changes in the header section. I have attached the complete header section as well as the line54.

Kindly check. Thanks for your quick response on this.

jmmut commented 3 years ago

oh, I see, Number=R was introduced in VCFv4.2. in VCFv4.1 you can only use number, A, G or dot. (see sections 1.2.2 https://samtools.github.io/hts-specs/VCFv4.1.pdf and https://samtools.github.io/hts-specs/VCFv4.2.pdf).

To make the VCF correct, try using VCFv4.2. Change the first line to:

fileformat=VCFv4.2

It looks like the validator is correct according to the specs, so I think this issue can be closed. Let me know if you think otherwise.

samarth51 commented 3 years ago

Yes, replacing VCFv4.1 to VCFv4.2 actually worked. We are validating our vcf's for EVS submission purpose. Kindly suggest if it is acceptable for submission purpose.

Thanks a lot for your help.

jmmut commented 3 years ago

I'm not sure if that was a typo, or if you mean to make an EVS (https://evs.gs.washington.edu/EVS/) submission to EVA (https://www.ebi.ac.uk/eva/?Submit-Data), or to make a submission to EVS.

If you mean to make a submission to EVA, all versions of VCF are accepted. We are not directly affiliated with EVS, so I can't say anything about it.

samarth51 commented 3 years ago

Surely that was a typo, I actually meant EVA (https://www.ebi.ac.uk/eva/?Submit-Data). We will make necessary changes and will validate again using vcf_validator then move ahead to EVA submission.

Again many thanks

EBIvariation / vcf-validator