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Before there is webpage for how to convert plink ped format to vcf
format. But it seems that this link disappeared.
Thank you very much in advance.
You cannot use the GATK to convert from ped to VCF. The link just advised people to use PlinkSeq.
I wrote a small script that uses plink to do the PED to VCF conversion:
The trickiest part, at least with my dataset, was orienting calls back to the reference strand. Hope this is helpful.