Command to flip snps

[Genetics189291]

What’s the command to flip snps when merging causes missing snps

[AimSmall]

Deja Vu


https://genarchivist.com/showthread.php?...1#pid18281

[AimSmall]

You can also take all of those steps are turn them into a function and do it in a single call.

Here is what Nganasankhan shared with me. Place these in your bashrc file.


plib()(plink --allow-no-sex --bfile "$@")
merg()(plib "$1" --bmerge "$2" --make-bed --out merge;plib "$2" --flip merge-merge.missnp --make-bed --out "$2-flip";plib "$1" --bmerge "$2-flip" --make-bed --out merge;plib "$2-flip" --exclude merge-merge.missnp --make-bed --out "$2-filtered";plib "$1" --bmerge "$2-filtered" --make-bed --out "${3-merged}")

Call it like this:
merg v62.0_HO_public AimSmall_genome