$ sed -i 1d filename
recode plink output for use in adegenet package of R
However, PLINK is designed for humans so it assumes there are 23 pairs of chromosomes unless you tell it otherwise. In some cases it will recognize:
$ --chr-set -dog
(to change it to the dog genome),
./plink --file batch_1.plink --recodeA --chr-set -dog
but you may also just need to tell it the number of chromosomes (as is the case of the zebra finch which has 30 chromosomes) with:
$ ./plink --file batch_1.plink --recodeA --allow-extra-chr --autosome-num 30
The --allow-extra-chr command allows for chromosome IDs that are non-standard.
This will output the plink.raw file that can be read into adegenet.