Exchange your double quotes for q( ) and that should do it.

system( q( ls -r1 *BC*.txt | grep -v Liver |awk '{split ($1,name,".");
+\
printf name[1]"\n"}' > BCfile.name" ) );
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Of course, you might want to question why you are going to all the trouble to write shell code in perl...

-sauoq
"My two cents aren't worth a dime.";