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    - /dependencies/VarDict/LICENSE
    - /dependencies/VarDict/README.rst
    - /dependencies/VarDict/checkCov.pl
    - /dependencies/VarDict/checkSNV.pl
    - /dependencies/VarDict/hg19_5k_150bpOL_seg.txt.gz
    - /dependencies/VarDict/joinLine
    - /dependencies/VarDict/minicheckCov.sh
    - /dependencies/VarDict/minicheckSNV.sh
    - /dependencies/VarDict/minivardict.sh
    - /dependencies/VarDict/minivardict_ion.sh
    - /dependencies/VarDict/my.bam
    - /dependencies/VarDict/my.bam.bai
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    - /dependencies/VarDict/pickLine
    - /dependencies/VarDict/runVarDict_BAM.sh
    - /dependencies/VarDict/sample2vardict.pl
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    - /dependencies/VarDict/splitBed2.pl
    - /dependencies/VarDict/testsomatic.R
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    - /dependencies/VarDict/var2vcf_paired.pl
    - /dependencies/VarDict/var2vcf_somatic.pl
    - /dependencies/VarDict/var2vcf_valid.pl
    - /dependencies/VarDict/vardict
    - /dependencies/VarDict/vardict.pl
    - /dependencies/VarDict/vardict2mut.pl
    - /dependencies/VarDict/vardict_sv.pl
    - /dependencies/VarDict/vcf2txt.pl
    - /dependencies/VarDict/waitVardict.pl
    - /dependencies/bam-readcount/bam-readcount
    - /dependencies/gatk/GenomeAnalysisTK.jar
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    - /dependencies/picard-tools-1.118/AddCommentsToBam.jar
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    - /dependencies/picard-tools-1.118/CleanSam.jar
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    - /dependencies/picard-tools-1.118/CollectWgsMetrics.jar
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    - /dependencies/picard-tools-1.118/CreateSequenceDictionary.jar
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    - /dependencies/picard-tools-1.118/ExtractIlluminaBarcodes.jar
    - /dependencies/picard-tools-1.118/ExtractSequences.jar
    - /dependencies/picard-tools-1.118/FastqToSam.jar
    - /dependencies/picard-tools-1.118/FilterSamReads.jar
    - /dependencies/picard-tools-1.118/FixMateInformation.jar
    - /dependencies/picard-tools-1.118/GatherBamFiles.jar
    - /dependencies/picard-tools-1.118/IlluminaBasecallsToFastq.jar
    - /dependencies/picard-tools-1.118/IlluminaBasecallsToSam.jar
    - /dependencies/picard-tools-1.118/IntervalListTools.jar
    - /dependencies/picard-tools-1.118/MakeSitesOnlyVcf.jar
    - /dependencies/picard-tools-1.118/MarkDuplicates.jar
    - /dependencies/picard-tools-1.118/MarkIlluminaAdapters.jar
    - /dependencies/picard-tools-1.118/MeanQualityByCycle.jar
    - /dependencies/picard-tools-1.118/MergeBamAlignment.jar
    - /dependencies/picard-tools-1.118/MergeSamFiles.jar
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    - /dependencies/picard-tools-1.118/ReorderSam.jar
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    - /dependencies/picard-tools-1.118/RevertSam.jar
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    - /dependencies/provean/src/Sequence.cpp
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    - /dependencies/provean/src/SequenceDB.cpp
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    - /dependencies/provean/src/Tables.cpp
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    - /dependencies/samtools-1.3/examples/00README.txt
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    - /dependencies/snpEff/examples/1kg.head_chr1.filtered.vcf.gz
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    - /dependencies/snpEff/examples/cancer.ann.vcf
    - /dependencies/snpEff/examples/cancer.eff.vcf
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    - /dependencies/snpEff/examples/cancer_pedigree.vcf
    - /dependencies/snpEff/examples/example_motif.vcf
    - /dependencies/snpEff/examples/examples.sh
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    - /dependencies/snpEff/examples/samples_cancer.txt
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    - /dependencies/snpEff/examples/test.1KG.ann_encode.vcf
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    - /dependencies/samtools-1.3/padding.o
    - /dependencies/samtools-1.3/phase.c
    - /dependencies/samtools-1.3/phase.o
    - /dependencies/samtools-1.3/sam.c
    - /dependencies/samtools-1.3/sam.h
    - /dependencies/samtools-1.3/sam.o
    - /dependencies/samtools-1.3/sam_header.c
    - /dependencies/samtools-1.3/sam_header.h
    - /dependencies/samtools-1.3/sam_header.o
    - /dependencies/samtools-1.3/sam_opts.c
    - /dependencies/samtools-1.3/sam_opts.h
    - /dependencies/samtools-1.3/sam_opts.o
    - /dependencies/samtools-1.3/sam_view.c
    - /dependencies/samtools-1.3/sam_view.o
    - /dependencies/samtools-1.3/sample.c
    - /dependencies/samtools-1.3/sample.h
    - /dependencies/samtools-1.3/sample.o
    - /dependencies/samtools-1.3/samtools
    - /dependencies/samtools-1.3/samtools.1
    - /dependencies/samtools-1.3/samtools.h
    - /dependencies/samtools-1.3/stats.c
    - /dependencies/samtools-1.3/stats.o
    - /dependencies/samtools-1.3/stats_isize.c
    - /dependencies/samtools-1.3/stats_isize.h
    - /dependencies/samtools-1.3/stats_isize.o
    - /dependencies/samtools-1.3/version.h
    - /dependencies/VarScan.v2.3.9.jar
    - /example/alignment/Sample1.bai
    - /example/alignment/Sample1.bam
    - /example/snpEff_ann/ENST00000269305.fasta
    - /example/snpEff_ann/Hotspots.txt
    - /example/snpEff_ann/transcripts.txt
    - /example/targetRegions/targetRegions.bed
    - /example/SampleNames.txt
    - /example/vcf_header.txt
    - /Scripte/00_intro.sh
    - /Scripte/01_gatk.sh
    - /Scripte/02_platypus.sh
    - /Scripte/03_varscan.sh
    - /Scripte/04_lofreq.sh
    - /Scripte/05_freebayes.sh
    - /Scripte/06_snver.sh
    - /Scripte/07_samtools.sh
    - /Scripte/08_vardict.sh
    - /Scripte/10_filter_target.R
    - /Scripte/11_normalize_calls.R
    - /Scripte/12_normalize_calls.R
    - /Scripte/20_annotate_known_ENST.R
    - /Scripte/30_normalize_calls.R
    - /Scripte/31_normalize_calls.R
    - /Scripte/40_combine_output.R
    - /Scripte/41_combine_output.R
    - /Scripte/50_determine_frequencies.R
    - /Scripte/51_combine_information.R
    - /Scripte/52_automatic_filtration1.R
    - /Scripte/53_check_databases.R
    - /Scripte/54_determine_effect_protein.R
    - /Scripte/55_automatic_filtration2.R
    - /Scripte/Call_Variants.sh
    - /Scripte/entrypoint.sh
    - /manual.md
    - /Config.sh
    - /LICENSE
    - /install.R
    - /Dockerfile
    - /README.md
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