Where to add --allow-no-sex in MakeReference (SNP2HLA)

Question

[khn]

Hello,

This might be the very basic question, but I have hard time adding "--allow-no-sex". I am doing as below in order to create the referece panel on SNP2HLA. I need to add "--allow-no-sex" somewhere below, but I could not succeed.

./MakeReference.csh /home/MYNAME/SNP2HLA_package_v1.0.3/MakeReference/MYFILE /home/MYNAME/SNP2HLA_package_v1.0.3/MakeReference//MYFILE_HLA.ped /home/MYNAME/SNP2HLA_package_v1.0.3/MakeReference/MYFILE_REF ./plink

Can anyone please teach me?

Thank you in advance!

Answer 1

[Philipp Bayer]

That's a PLINK command - you could replace this line (inside MakeReference.csh)

alias plink '$4 --noweb --silent'

by

alias plink '$4 --noweb --silent --allow-no-sex'

[khn]

Thank you so much. It worked very well!! Thank you again!