gatk-3.8/perl/1kgScripts/runPilotPipelines.sh

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#perl /humgen/gsa-scr1/ebanks/Sting/perl/1kgScripts/runPilot1Pipeline.pl -i /humgen/gsa-hphome1/projects/1kg_pilot1/mergedBamsByPopulation -o /broad/hptmp/ebanks/1kg_pilot1/cleaned -dry
perl /humgen/gsa-scr1/ebanks/Sting/perl/1kgScripts/runPilot2Pipeline.pl -i /broad/1KG/DCC_merged/freeze5.2 -o /broad/hptmp/ebanks/1kg_pilot2/cleaned -dry