drwxr-xr-x	root/root	usr/
drwxr-xr-x	root/root	usr/bin/
lrwxrwxrwx	root/root	usr/bin/SnpSift.jar -> ../lib/snpeff/SnpSift.jar
lrwxrwxrwx	root/root	usr/bin/snpEff.jar -> ../lib/snpeff/snpEff.jar
drwxr-xr-x	root/root	usr/lib/
drwxr-xr-x	root/root	usr/lib/snpeff/
-rw-rw-r--	root/root	usr/lib/snpeff/SnpSift.jar
drwxrwxr-x	root/root	usr/lib/snpeff/examples/
-rw-rw-r--	root/root	usr/lib/snpeff/examples/1kg.head_chr1.filtered.vcf.gz
-rw-rw-r--	root/root	usr/lib/snpeff/examples/1kg.head_chr1.vcf.gz
-rw-rw-r--	root/root	usr/lib/snpeff/examples/cancer.ann.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/cancer.eff.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/cancer.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/cancer_pedigree.ann.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/cancer_pedigree.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/example_motif.vcf
-rwxrwxr-x	root/root	usr/lib/snpeff/examples/examples.sh
-rw-rw-r--	root/root	usr/lib/snpeff/examples/file.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/intervals.bed
-rw-rw-r--	root/root	usr/lib/snpeff/examples/my_annotations.bed
-rw-rw-r--	root/root	usr/lib/snpeff/examples/samples_cancer.txt
-rw-rw-r--	root/root	usr/lib/snpeff/examples/samples_cancer_one.txt
-rw-rw-r--	root/root	usr/lib/snpeff/examples/test.1KG.ann_encode.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/test.1KG.ann_reg.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/test.1KG.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/test.ann.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/test.chr22.ann.filter_missense.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/test.chr22.ann.filter_missense_any.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/test.chr22.ann.filter_missense_any_TRMT2A.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/test.chr22.ann.filter_missense_first.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/test.chr22.ann.one_per_line.txt
-rw-rw-r--	root/root	usr/lib/snpeff/examples/test.chr22.ann.txt
-rw-rw-r--	root/root	usr/lib/snpeff/examples/test.chr22.ann.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/test.chr22.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/test.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/variants_1.ann.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/variants_1.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/variants_2.ann.vcf
-rw-rw-r--	root/root	usr/lib/snpeff/examples/variants_2.vcf
drwxrwxr-x	root/root	usr/lib/snpeff/galaxy/
-rw-rw-r--	root/root	usr/lib/snpeff/galaxy/snpEff.xml
-rwxrwxr-x	root/root	usr/lib/snpeff/galaxy/snpEffWrapper.pl
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-rwxrwxr-x	root/root	usr/lib/snpeff/galaxy/snpSiftWrapper.pl
-rw-rw-r--	root/root	usr/lib/snpeff/galaxy/snpSift_annotate.xml
-rw-rw-r--	root/root	usr/lib/snpeff/galaxy/snpSift_caseControl.xml
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-rw-rw-r--	root/root	usr/lib/snpeff/galaxy/snpSift_int.xml
drwxrwxr-x	root/root	usr/lib/snpeff/galaxy/tool-data/
-rw-rw-r--	root/root	usr/lib/snpeff/galaxy/tool-data/snpEff_genomes.loc
-rw-rw-r--	root/root	usr/lib/snpeff/galaxy/tool-data/snpEff_genomes.loc.sample
-rw-rw-r--	root/root	usr/lib/snpeff/galaxy/tool_conf.xml
-rw-rw-r--	root/root	usr/lib/snpeff/galaxy/tool_dependencies.xml
drwxrwxr-x	root/root	usr/lib/snpeff/scripts/
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/1kg.sh
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/annotate_demo.sh
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/annotate_demo_GATK.sh
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/bedEffOnePerLine.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/buildDbNcbi.sh
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/cgShore.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/cgShore.sh
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/countColumns.py
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/db.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/extractSequences.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/fasta2tab.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/fastaSample.pl
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-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/fastqSplit.pl
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-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/gffRemovePhase.pl
drwxrwxr-x	root/root	usr/lib/snpeff/scripts/gsa/
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/gsa/bayesFactor_correction_scoreCount.r
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/gsa/bayesFactor_correction_scoreCount.sh
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/gsa/bayesFactor_correction_scoreCount_max10.sh
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/gsa/checkGeneNames.py
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/gsa/create_sets.bds
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/gsa/geneSetOverlap.py
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-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/gsa/pvalue_correction_scoreCount.sh
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/gsa/pvalue_correction_scoreCount_min10.sh
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/isutf8.py
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/join.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/joinSnpEff.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/make_dbNSFP.sh
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/nextProt_filter.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/ped2vcf.py
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/plot.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/plotHistogram.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/plotLabel.pl
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-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/plotQQ.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/plotQQsubsample.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/plotSmoothScatter.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/plotXY.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/queue.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/sam2fastq.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/snpEff
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/snpSift_filter_sample_to_number.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/sortLine.py
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/splitChr.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/statsNum.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/swapCols.pl
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-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/txt2fa.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/txt2vcf.py
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-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/uniqCut.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/vcfAnnFirst.py
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/vcfBareBones.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/vcfEffHighest.ORI.py
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/vcfEffOnePerLine.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/vcfFilterSamples.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/vcfInfoOnePerLine.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/vcfOnlyAlts.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/vcfReduceGenotypes.pl
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/vcfRefCorrect.py
-rwxrwxr-x	root/root	usr/lib/snpeff/scripts/wigSplit.pl
-rw-rw-r--	root/root	usr/lib/snpeff/snpEff.config
-rw-rw-r--	root/root	usr/lib/snpeff/snpEff.jar