\ is being used as an escape character, the variables are being used insert values within parts of the strings (see String_interpolation). Basically the program is building a command which gets called by system. You can output the command to screen easily by replacing the system call with a print, like so

print "awk \'\$1 == \"$label\" && \$3 <= $apex && \$4 >= $apex\{print\
+}\' $reference >temp_marker_$name";
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