Produces invalid VCF - Githubissues

Hi,

I ran the produced VCF through the VCF validator (debugulator) here: https://github.com/EBIvariation/vcf-validator

Unfortunately it gave the following error:

According to the VCF specification, the input file is not valid
Error: The fileformat declaration is not valid (the line must start with 
##fileformat= and the value must be one of 'VCFv4.1', 'VCFv4.2' or 'VCFv4.3').
This occurs 1 time(s), first time in line 1.

I added ##fileformat=VCFv4.1

There are a few more errors after I've fixed this one:

This occurs 1 time(s), first time in line 25.

I added ##reference=GCF_000001405.13

I then added the contigs:

##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT>

Now I get 803 errors like this:

Error: Duplicated variant 1:2526746:A>G found. This occurs 2 time(s), first time in line 468.

which relates to these rows:

1   2526746 rs3748816   A   G   .   .   .   GT  1/1
1   2526746 i6059967    A   G   .   .   .   GT  1/1

From the spec I think this should be:

1   2526746 rs3748816;i6059967  A   G   .   .   .   GT  1/1

I 'fixed' these using the debugulator.

Now I notice:

Warning: FORMAT 'GT' is not listed in a valid meta-data FORMAT entry. This occurs 948928 time(s), first time in line 51.

So I added:

##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

It then complains about all 'non standard' comments, which I don't think is correct... However, I stripped them out.

The final header I created looks like this:

##fileformat=VCFv4.1
##fileDate=16-02-22
##source=GenomePrep v1.1,company=23andme,usebadallele=c4,maxcov=1.0,from_valid_snps=959109
##reference=GCF_000001405.13
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=Assembly>
##contig=<ID=11,length=Assembly>
##contig=<ID=12,length=Assembly>
##contig=<ID=13,length=Assembly>
##contig=<ID=14,length=Assembly>
##contig=<ID=15,length=Assembly>
##contig=<ID=16,length=Assembly>
##contig=<ID=17,length=Assembly>
##contig=<ID=18,length=Assembly>
##contig=<ID=19,length=Assembly>
##contig=<ID=20,length=Assembly>
##contig=<ID=21,length=Assembly>
##contig=<ID=22,length=Assembly>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  90365083240

I'm pointing this out because I'm seeing an error when uploading the VCF here: https://imputationserver.sph.umich.edu/index.html#!pages/home

and I get the fatal error:

Input Validation
The provided files are not VCF files (see Help).

changlubio / GenomePrep

Produces invalid VCF #2