--mach-r2-filter

[test1]

Not sure if the new function (--mach-r2-filter ) in plink2 alpha, can filter the R2 values located inside MIS style vcf files (Michigan imputation server-vcf file format).

I enclosed an example .

if yes, appreciate if you send complete command line.

thank you again!

b.

[Christopher Chang]

Well, if the R2 value is already in the VCF INFO column, it's easy to filter on it with a short script.  But, as long as you include "dosage=DS" in your VCF import command (e.g. "plink2 --vcf example.vcf dosage=DS --mach-r2-filter 0.3 --make-pgen --out filtered_dataset", --mach-r2-filter will also work properly (by computing R2 from scratch).

[test1]

That is great!...thank you...I guess make-bed can also be applied here...