Entering edit mode
10.2 years ago
neilclelland
•
0
Hi,
I would like to know if it is possible to output .ld results as a delimited text file rather than the space delimited file that is produced as default.
I have around 13k snp's which I have ld results on (around 88 million rows) and I want to import the file back into sql. There are ways of doing this by creating a formatted file and bulk inserting that, but I wondered if it would be possible to change the output format of the results file in PLINK as this would make the bulk insert into sql simpler.
My current code is:
plink --noweb --bfile myfile --cow --missing-genotype - --ld-window-r2 0
Any advice would be great
Neil
There doesn't appear to be a way to do this from PLINK but I found this, which was very helpful.
http://www.gettinggeneticsdone.com/2010/08/convert-plink-output-to-tab-or-comma.html
Neil