exporting dosage in VCF file

[Sarah Medland]

Hi

I'm testing out the vcf export options to generate minimac3 style vcf files using  "--export vcf vcf-dosage=DS "

The output is patchy - most snp*individual entries have GT only some have GT:DS and some have DS only (screen shot of a section of data below showing the various combinations)
This output will not be readable by downstream programs as a minimac3 style vcf.

Any suggestions on how to obtain consistent GT:DS data from plink2?

thanks
Sarah

[Christopher Chang]

Hmm, the current output should conform to the VCF spec?  (Omitted field = missing value, and DS is omitted if and only if it's an integer that can be inferred exactly from GT.)

With that said, I realize that some minimac3 VCF readers may not be able to handle this.  It would substantially increase the size of the output file, but I can add an option this weekend to dump redundant DS values.

(With that said, the current output should conform to the VCF spec?)

[Sarah Medland]

That would be great - I realise it is going to increase size a lot but there are a number of tools that can't deal with this.

If you are willing to consider adding another option, the ability to output a vcf that contains DS but not GT is also readable by many programs and would help keep the size down.

best wishes
Sarah

[Christopher Chang]

vcf-dosage=DS-force is now implemented; let me know if you run into any problems with it.

(I don't plan to add any sort of omit-GT option, since that creates problems on chrX...)

[Sarah Medland]

Wonderful - thanks!