[GenABEL-dev] Specifying chromosome number during upload

[CORBIN Laura]

Hi all, 

I was wondering if it would be possible to add an option to specify the number of chromosomes and whether X, Y, mt, etc are included when uploading data to GenABEL.  Currently I use the convert.snp.tped with .tped and .tfam files from Plink.  The problem is that when Plink makes the transpose files it replaces 'X' with a number, in my case 32, but GenABEL needs it to be 'X' in order to recognise it as a sex chromosome.  It's relatively straight forward to edit the files before loading them but it would be neat if they could be read straight in.

Thanks

Laura



The Roslin Institute has moved!

Please contact me at our new offices:

Division of Genetics and Genomics
The Roslin Institute 
The University of Edinburgh
Easter Bush Campus
Midlothian
EH25 9RG
Scotland, UK 

By Telephone: 
+44 (0)131 651 9221

 
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336
Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. 

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.