17 lines
849 B
Bash
Executable File
17 lines
849 B
Bash
Executable File
#!/bin/bash
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rm -f *.txt
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export GSA_ROOT_DIR=/home/karthikg/broad/gsa-unstable
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#-Djava.library.path is needed if you are using JNI_LOGLESS_CACHING, else not needed
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java -Djava.library.path=${GSA_ROOT_DIR}/PairHMM_JNI -jar ${GSA_ROOT_DIR}/dist/GenomeAnalysisTK.jar -T HaplotypeCaller \
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-R /data/broad/samples/joint_variant_calling/broad_reference/Homo_sapiens_assembly19.fasta \
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-I /data/simulated/sim1M_pairs_final.bam \
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--dbsnp /data/broad/samples/joint_variant_calling/dbSNP/00-All.vcf \
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-stand_call_conf 50.0 \
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-stand_emit_conf 10.0 \
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--pair_hmm_implementation JNI_LOGLESS_CACHING \
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-o output.raw.snps.indels.vcf
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#--pair_hmm_implementation JNI_LOGLESS_CACHING \
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#-I /data/simulated/sim1M_pairs_final.bam \
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#-I /data/broad/samples/joint_variant_calling/NA12878_low_coverage_alignment/NA12878.chrom11.ILLUMINA.bwa.CEU.low_coverage.20121211.bam \
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