Quality check for illumina GSA data

Question

[xinhui.wang]

Dear all, I have many illumina GSA (iscan) data, I would like to check is these any sample contaminated? Is there some tool in linux could do in command line? Thanks and with best regards, Xinhui

Answer 1

[brinderbuttar]

Hi Xinhui, I am also looking for solution to the problem you shared few years back. I suppose you might figured out the answer also. People are recommending PLINK for that, if you have anything else, please let me know. Thanks in advance Brinder