SamToIGV.pbs

#!/bin/bash                                                                    
#PBS -l nodes=1:ppn=8,walltime=1:00:00                                        
#PBS -N SamToIGV                                                       
#PBS -M ${USER}@nyu.edu                                                        
#PBS -m abe                                                                   
#PBS -o localhost:/scratch/$USER/${PBS_JOBNAME}.o${PBS_JOBID}                
#PBS -e localhost:/scratch/$USER/${PBS_JOBNAME}.o${PBS_JOBID}                 

cd /scratch/$USER

module load samtools/intel/1.2

TAG1=$arg2 ## write on command line, example AH6407A-120412-Try1
TAG2=$arg1 ## write on command line, folder name where SAM file is found

cd ${TAG2}

samtools view -b -S -o ${TAG1}.bam ${TAG1}.sam
samtools sort ${TAG1}.bam ${TAG1}.sorted
samtools index ${TAG1}.sorted.bam

exit 0;