gnuplot from stdin

drio@milhouse:/mnt/slx/bfast_related/test.bwa.bf2.ecoli $ head test.txt 
Chr1    2       G       G       30      0       60      1       ^~.     E
Chr1    3       C       C       30      0       60      1       .       E
Chr1    4       T       T       30      0       60      1       .       E
Chr1    5       T       T       30      0       60      1       .       E
Chr1    6       T       T       30      0       60      1       .       E
Chr1    7       T       T       30      0       60      1       .       E
Chr1    8       C       C       30      0       60      1       .       E
Chr1    9       A       A       30      0       60      1       .       E
Chr1    10      T       T       33      0       60      2       .^~.    EE
Chr1    11      T       T       33      0       60      12      ..      E"
drio@milhouse:/mnt/slx/bfast_related/test.bwa.bf2.ecoli $ (echo "set t png";echo plot \"-\" using 1:2 notitle with lines; cat test.txt | awk '{print $2" "$8}') | gnuplot > output.png

# Another example (plot snp quality distributions)

$ for i in `find . -name "merged*.pileup"`; do (echo "set t png";echo plot \"-\" using 2:1 notitle; cat $i | grep -v "\*"| awk '{print $5}' | sort -n | uniq -c ) | gnuplot > $i.png  ; done