#!/bin/bash
#PBS -l walltime=00:30:00
#PBS -l nodes=1:ppn=8
#PBS -l vmem=2000mb

#  runSamtoolsMerge.pbs
#
#  Created by Ivory on 10/24/14.
#

# This is one of three components: callRunSamtoolsMerge.sh, runSamtoolsMerge.pbs, and SampleRuns.txt
# all three of these files work together to merge the correct bam files for each sample.

# Pass in these variables via qsub
# bamOUT=fileName.bam for output
# bamIN=fileNames string for input bam files

cd $PBS_O_WORKDIR

samtools merge $bamOUT $bamIN
samtools index $bamOUT