Question: Convert .Pre Files To .Ped And .Map Files For Plink
1
gravatar for Nandini
7.5 years ago by
Nandini830
London
Nandini830 wrote:

Hello,

For association studies, I have the genotype data in .pre, .dat and .map (pre make-ped format) and I would like to convert it to plink format (.ped, .map or .bam .bim. fam).

Is there any way of doing this ? I tried using "makeped" but I ended up getting errors :

ERROR: Ped: 70855 Per: 1 - No family

Thank you.

plink • 5.9k views
ADD COMMENTlink modified 5.3 years ago by dweeks.pitt40 • written 7.5 years ago by Nandini830
2

Here's a tutorial that uses .pre and .map-files as entry for PLINK and shows how to convert them, maybe that helps: http://www.vipbg.vcu.edu/~sarahme/eg/c16/practicals_C16.pdf

ADD REPLYlink modified 7.5 years ago by Istvan Albert ♦♦ 81k • written 7.5 years ago by Philipp Bayer6.5k

Thank you. The .pdf was very useful.

The .pre files is pretty much like the .ped format

FAM001 1 0 0 1 2 A A G G A C

FAM001 2 0 0 1 2 A A A G A C

I also tried to just change the extension by .pre to .ped and PLINK accepted that.

Also some of my markers contain more than 2 alleles which is not acceptable by PLINK - is there any way of dealing with this ?

ADD REPLYlink modified 7.5 years ago • written 7.5 years ago by Nandini830
2

So you have something like rs1214214 with A, T and G? Sounds dodgy.

I'd just skip markers having more than 2 alleles, I hope you don't have many of these...

ADD REPLYlink written 7.5 years ago by Philipp Bayer6.5k

Sample data would be helpful. http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped

ADD REPLYlink written 7.5 years ago by zx87548.4k
0
gravatar for dweeks.pitt
5.3 years ago by
dweeks.pitt40
United States
dweeks.pitt40 wrote:

The Mega2 program can convert from pre-makeped LINKAGE format to PLINK format.

See: http://watson.hgen.pitt.edu/docs/conversions/linkage_plink.html

ADD COMMENTlink written 5.3 years ago by dweeks.pitt40
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