Question
Question Posted 02/14/20:
Hi,
I processed plink file of ADNIGO-2, noticing chr0-25, and dict says 1-22, X, Y, XY, MT. so chr23 is X and Chr24 is Y, is it right? However, when I sexcheck, it tells 16778 Xchr and 0 Ychr variant(s) scanned. When I grep -X from the plink file I got SNPs from Chr23, but I can't grey -Y from plink file from Chr24. How so? Is there anything I can do to identify the Y in Chr24 so I won't get problem at sexcheck?
Thanks !!!
Hi,
I processed plink file of ADNIGO-2, noticing chr0-25, and dict says 1-22, X, Y, XY, MT. so chr23 is X and Chr24 is Y, is it right? However, when I sexcheck, it tells 16778 Xchr and 0 Ychr variant(s) scanned. When I grep -X from the plink file I got SNPs from Chr23, but I can't grey -Y from plink file from Chr24. How so? Is there anything I can do to identify the Y in Chr24 so I won't get problem at sexcheck?
Thanks !!!
Response posted 02/19/20 by Kwangsik Nho:
Please see this: http://zzz.bwh.harvard.edu/plink/summary.shtml#sexcheck
