--vcf-half-call

[Sandra Barral]

Hi All,

When converting my vcf file into plink binary files, it seems there are half calls so I am trying to use the  --vcf-half-call  command to set them as missing

plink2 --vcf myfile.vcf --vcf-half-call missing'/'m --make-bed --out myfile

however, I get the following error

Error: 'missing/m' is not a valid mode for --vcf-half-call

Hoping someone can help!

thanks in advance!

[Christopher Chang]

Either "--vcf-half-call m" or "--vcf-half-call missing" should work; sorry if that was unclear.

[Sandra Barral]

thanks, that seems to work now!