phased-vcf to ped

[bn]

chris:

I have a phased vcf data and I want to change it to ACGT , ped file. 

when I use --vcf --recode, the out put ped file doesn't seem to distinguish HTZ orders (CG versus GC)...all are CG.  I want to generate haplotypes using haploview and so this will be issue...

what I am doing wrong...

thanks,

b.

[Christopher Chang]

Phase is not supposed to be defined in the .ped format, so you'll need to use another tool/script to generate this type of nonstandard .ped.