create_vcf does not follow the GWAS VCF format specification?

[MalteThodberg]

Looking at the GWASVCF specification in https://github.com/MRCIEU/gwas-vcf-specification, it looks like create_vcf doesn't quite follow these conventions:

• create_vcf creates an ExpandedVCF class with multi-allelic SNPs, even though the format specification says it should only be single bi-allelic SNP on each line
• create_vcf calls sample size "SS" and the specification calls sample size "NS"
• create_vcf doesn't include all the reserved fields, it is missing: EZ, SI and AC.

[mcgml]

Hi @MalteThodberg

Thanks for raising this. The create_vcf function is producing GWAS-VCF using spec v1.0 which is available from here. We aim to update the code to the latest version of spec in the future. I will update this repo to make clearer.

Sorry for the confusion

Thanks
Matt

[MalteThodberg]

cool!

Also one more thing: create_vcf doesn't require ES, SE and LP even though they are listed as required fields

[mcgml]

@explodecomputer can you answer @MalteThodberg question? I have created a PR for the docs