.dose format to bed/bim/fam
290 views
Skip to first unread message
Jiang
Aug 10, 2016, 10:00:07 AM8/10/16
to plink2-users
Hi,
I'm trying to convert from PLINK dosage format (.dose + .fam) to bed/bim/fam ("best guess genotypes").
A Google search indicates that this can be done using fcGENE; has any of you experience with it? (When I tried it, I had the same issue as https://www.biostars.org/p/58301/ .)
Or maybe there's a way using PLINK directly? (I cannot figure it out.)
Any suggestions would be highly appreciated.
Thanks in advance,
I'm trying to convert from PLINK dosage format (.dose + .fam) to bed/bim/fam ("best guess genotypes").
A Google search indicates that this can be done using fcGENE; has any of you experience with it? (When I tried it, I had the same issue as https://www.biostars.org/p/58301/ .)
Or maybe there's a way using PLINK directly? (I cannot figure it out.)
Any suggestions would be highly appreciated.
Thanks in advance,
Christopher Chang
Aug 11, 2016, 2:47:19 AM8/11/16
to plink2-users
This is not supported by PLINK 1.x. The only dosage format which PLINK 1.x can directly convert to best-guess phenotypes, or perform probabilistic conversions of, is Oxford .gen/.bgen.
Christopher Chang
Aug 11, 2016, 4:46:16 PM8/11/16
to plink2-users
However, there is a standalone dose2plink program which may do what you want. The original is at https://www.genepi.qimr.edu.au/staff/sarahMe/dose2plink.html (expired SSL certificate, but nothing nasty there); a C port I wrote is at https://github.com/chrchang/plink-ng/blob/master/dose2plink.c .
On Wednesday, August 10, 2016 at 7:00:07 AM UTC-7, Jiang wrote:
Reply all
Reply to author
Forward
0 new messages