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Modified run.sh

This commit is contained in:
Karthik Gururaj 2014-01-27 14:56:46 -08:00
parent 2c0d70c863
commit a15137a667
1 changed files with 1 additions and 1 deletions
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public/c++/VectorPairHMM/run.sh
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@ -8,7 +8,7 @@ then
fi fi
#-Djava.library.path is needed if you are using JNI_LOGLESS_CACHING, else not needed #-Djava.library.path is needed if you are using JNI_LOGLESS_CACHING, else not needed
java -Djava.library.path=${GSA_ROOT_DIR}/PairHMM_JNI/ -jar $GSA_ROOT_DIR/dist/GenomeAnalysisTK.jar -T HaplotypeCaller \ java -Djava.library.path=${GSA_ROOT_DIR}/public/c++/VectorPairHMM -jar $GSA_ROOT_DIR/dist/GenomeAnalysisTK.jar -T HaplotypeCaller \
--dbsnp /data/broad/samples/joint_variant_calling/dbSNP/00-All.vcf \ --dbsnp /data/broad/samples/joint_variant_calling/dbSNP/00-All.vcf \
-R /opt/Genomics/ohsu/dnapipeline/humanrefgenome/human_g1k_v37.fasta \ -R /opt/Genomics/ohsu/dnapipeline/humanrefgenome/human_g1k_v37.fasta \
-I /data/simulated/sim1M_pairs_final.bam \ -I /data/simulated/sim1M_pairs_final.bam \