Closed CholoTook closed 2 years ago
Hi there,
The header file was messy, thanks for pointing it out. It was originally simply copied from the consumer genome metadata, but these don't fit the VCF format.
The fatal error in the end was caused by duplicate lines from the consumer genome data (seen in many cases in 23andMe output, but they usually have the same genotyping calls just different rsids).
I have fixed the bugs above and tested using vcf_validator. Let me know if it fails again :)
Cheers C
Hi,
I ran the produced VCF through the VCF validator (debugulator) here: https://github.com/EBIvariation/vcf-validator
Unfortunately it gave the following error:
I added
##fileformat=VCFv4.1
There are a few more errors after I've fixed this one:
I added
##reference=GCF_000001405.13
I then added the contigs:
Now I get 803 errors like this:
which relates to these rows:
From the spec I think this should be:
I 'fixed' these using the debugulator.
Now I notice:
So I added:
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:
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: