Using GATK convert ped to vcf

Jinyan

Before there is webpage for how to convert plink ped format to vcf format. But it seems that this link disappeared.

http://www.broadinstitute.org/gsa/wiki/index.php/Converting_ped_to_vcf

Thank you very much in advance.

ebanks

You cannot use the GATK to convert from ped to VCF. The link just advised people to use PlinkSeq.

chapmanb

I wrote a small script that uses plink to do the PED to VCF conversion:

https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/plink_to_vcf.py

The trickiest part, at least with my dataset, was orienting calls back to the reference strand. Hope this is helpful.