rs36810213_HET   rs2438689   rs70927523570_HET   rs54666437   ...
1                0           2                   0
0                1           0                   1
2                0           1                   1
...              ...         ...                 ...

rs2438689   rs54666437   ...
0           0
1           1
0           1
...         ...

#!/bin/bash

path="/data/folder"

awk -v OFS='t' '

NR==1{
    for (i=1;i<=NF;i++)
        if ($i=="_HET") {
            n=i-1
            m=NF-(i==NF)
        }
    }

{
    for(i=1;i<=NF;i+=1+(i==n))
        printf "%s%s",$i,i==m?ORS:OFS
}

' $path/input.txt >> $path/output.txt