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samesense/gist:71449e0a3e0467bec4c1

Created December 17, 2015 15:56
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gistfile1.txt
/mnt/isilon/cbmi/variome/bin/java -Xmx32g -Xms16g -jar /mnt/isilon/cbmi/variome/bin/GenomeAnalysisTK-1.6-2-gc2b74ec/3.3-0/GenomeAnalysisTK.jar -l DEBUG -variant_index_type LINEAR -variant_index_parameter 128000 --emitRefConfidence GVCF -T HaplotypeCaller -R /mnt/isilon/cbmi/variome/reference/mm9.fa -I ~/me/projects/blobel/download_encode/data/bam_group/ENCFF001NTS.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 -o /home/evansj/me/projects/blobel/download_encode/data/gvars/ENCFF001NTS.g.vcf
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