Entering edit mode
3 months ago
Hi!
I'm trying to merge 1000g data with my own. I got a warning saying "multiple chromosomes seen for variant "rs______" and this was the case for 10012 variants. I tried --flip and it didn't work well, so I decided to exclude those variants. Afterwards, when I tried to merge with the excluded files, I got a lot of errors of variants 'rs____" and "rs_____" have the same position. I checked out what was the issue, and for some of them the problem is that one of the RSID has merged into a different name (example: rs62240042 has merged into rs9616839). How can I fix this issue? When I merge it the second time, the merge works, but the genotyping rate is only 0.63 which is much lower.
Thanks so much!
