I have this line
samtools view -h file | awk '$3=="chr$a" || /^@/' | samtools view -S - -b -o output
the dash between the -S and the -b is supposed to indicate to the program that it is from STDIN. I can run it from a perl script on the command line but as soon as I try to move it into a shell script it just creates the file without outputting any data. Any ideas would be greatly appreciated.