Get ambiguous alleles

ambiguous_alleles.sh

#Assumes data is a table delimited .bim file
bimfile=bim_name_here
grep -P "A\tT" $bimfile > ambiguous_snps.txt
grep -P "T\tA" $bimfile >> ambiguous_snps.txt
grep -P "C\tG" $bimfile >> ambiguous_snps.txt
grep -P "G\tC" $bimfile >> ambiguous_snps.txt


#for metal
 bimfile=LOOMeur_1_.results
grep -P "\ta\tt\t" $bimfile > ambiguous_snps.txt
grep -P "\tt\ta\t" $bimfile >> ambiguous_snps.txt
grep -P "\tc\tg\t" $bimfile >> ambiguous_snps.txt
grep -P "\tg\tc\t" $bimfile >> ambiguous_snps.txt
awk '{print $1}' ambiguous_snps.txt > ambiguous_snps2.txt