Running samtools pileup on some aligned reads

samtools needs a sorted file for pileup.. doesn't give you an error if it isn't sorted so watch out!

./samtools faidx phi.fa
./samtools import ./phi.fa.fai /scratch/nava/lane7.phi.sam /scratch/nava/lane7.phi.bam
./samtools sort /scratch/nava/lane7.phi.bam /scratch/nava/lane7.phi.bam.sort
./samtools pileup -f ./phi.fa /scratch/nava/lane7.phi.bam.sort.bam > pile