How to convert Plink case-control to Merlin format?

[Ana Marija]

Hello,

I was following your instructions given here:

https://docs.google.com/viewer?a=v&pid=forums&srcid=MDU3MzMwODU3ODIzNjAwNDk5NzIBMTQ5MDI0MjYxMTE3ODQxNDM3MDgBMHhObXRNRkRFUUFKATAuMQEBdjI&authuser=0

My log file is in attach. Also my Plink files are in current directory:outputZ11.bim,outputZ11.fam,outputZ11.bed

Pheno is not present in those file and this is case-control study.

.fam file looks like this:

head outputZ11.fam
fam0110    G110    0    0    0    -9
fam0113    G113    0    0    0    -9
fam0114    G115    0    0    0    -9
fam0114    G116    0    0    0    -9
fam0117    G117    0    0    0    -9
fam0118    G118    0    0    0    -9

Can you please tell me how to run this in order to convert these files to Merlin format?

Cheers,

Ana

[Dan Weeks]

Dear Ana,

While the error message is not very informative and should be improved, it looks like it is trying to open a file without a name ('null') for reading and it can't.

You are getting this because you didn't also provide a PLINK-format bim map file, as required:

 4) Binary data file:  (PLINK .bed) [required] _

 5) Pedigree file:     (PLINK .fam) [required] _

 6) PLINK map file:    (PLINK .bim) [required] _

So if you give it the trio of a bed, fam, and bim files as input, it should then work for you.

I hope you find Mega2 useful in your research.

Thanks,

-- Dan --