Reference and Alternative Allele assignment when plink transfer PED format to VCF format

[Shicheng Guo]

Hi Chris, 

How plink to assign reference allele and alternative allele when transfer PED format to VCF format? 

Thanks

Shicheng

[Christopher Chang]

It doesn't; plink 1.x does not have a real notion of ref vs. alt allele.  All lines in the body of a VCF generated from a PED should have the INFO:PR flag, which has the description "Provisional reference allele, may not be based on real reference genome".

If your file contains only SNPs, you can use plink 2.0's --ref-from-fa command to set the correct reference alleles, and as long as you stick to plink2's .pgen file format or only use plink2 to work with the .bed+.bim+.fam, they will remain correct for later VCF export.  But as soon as you use plink 1.x to work with the data, you should expect reference allele information to be lost.