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titleMake job submission script for mapping & variant calling
echo "align_bwa.sh $BI/ngs_course/human_variation/allseqs_R1.fastq test hg19 1 > aln.test.log 2>&1" > commands
launcher_creator.py -l map_call.sge -n map_call -t 01:00:00 -j commands
module load bwa/0.5.9
module load samtools
qsub map_call.sge

Caution: If you are using this example outside an SSC course, you must use the -a option to specify a valid allocation (e.g. BME_2012)

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