export file format in vcf.gz

[Mere H]

Hi PLINK community,

I am wondering if PLINK can export the file in vcf.gz format? I know the following code can export vcf, and then I can use bgzip to zip the vcf, but is there a way to get vcf.gz directly as the output so that we can avoid letting the vcf take much storage space in the first place?

--export vcf 'vcf-dosage=HDS-force' --out filename

I have also noticed that vcf.gz can be imported by using --vcf, just in the same way as importing vcf. If vcf.gz is an acceptable import format, I guess there must be a way to export this format as well, right?

Thank you!

Mey

[Christopher Chang]

You're looking for "--export vcf bgz ..."

[Mere H]

Thanks, Dr. Chang! That works well and serves my purpose. 

Here is the code I used with success:

--export vcf 'bgz' 'vcf-dosage=HDS-force' --out filename

Mey