LICENSE.txt
README.md
setup.cfg
setup.py
r_scripts/__init__.py
r_scripts/ada_cross_validation.R
r_scripts/ada_model_builder.R
r_scripts/ada_model_builder_ntChange.R
r_scripts/ada_model_predictor.R
r_scripts/xgboost_model_builder_ntChange.R
r_scripts/xgboost_model_predictor.R
somaticseq/SSeq_tsv2vcf.py
somaticseq/__init__.py
somaticseq/_version.py
somaticseq/annotate_caller.py
somaticseq/combine_callers.py
somaticseq/ntchange_type.py
somaticseq/run_somaticseq.py
somaticseq/sequencing_features.py
somaticseq/single_sample_vcf2tsv.py
somaticseq/somatic_vcf2tsv.py
somaticseq/somatic_xgboost.py
somaticseq/somaticseq_parallel.py
somaticseq/tsv2vcf.py
somaticseq.egg-info/PKG-INFO
somaticseq.egg-info/SOURCES.txt
somaticseq.egg-info/dependency_links.txt
somaticseq.egg-info/requires.txt
somaticseq.egg-info/top_level.txt
somaticseq/genomicFileHandler/__init__.py
somaticseq/genomicFileHandler/concat.py
somaticseq/genomicFileHandler/genomic_file_handlers.py
somaticseq/genomicFileHandler/pileup_reader.py
somaticseq/genomicFileHandler/read_info_extractor.py
somaticseq/utilities/BAM_filter.py
somaticseq/utilities/__init__.py
somaticseq/utilities/attach_pileupVAF.py
somaticseq/utilities/bamQC.py
somaticseq/utilities/bedFileHandler.py
somaticseq/utilities/combo_callers_evaluator.py
somaticseq/utilities/filter_SomaticSeq_VCF.py
somaticseq/utilities/linguistic_sequence_complexity.py
somaticseq/utilities/lociCounterWithLabels.py
somaticseq/utilities/lociCounters.py
somaticseq/utilities/multi-nucleotide_phaser.py
somaticseq/utilities/paired_end_bam2fastq.py
somaticseq/utilities/plot_TPvsFP.py
somaticseq/utilities/reformat_VCF2SEQC2.py
somaticseq/utilities/remove_callers_from_somaticseq_tsv.py
somaticseq/utilities/split_Bed_into_equal_regions.py
somaticseq/utilities/split_mergedBed.py
somaticseq/utilities/tally_MyVCF_vs_Truth.py
somaticseq/utilities/tally_variants_from_multiple_vcfs.py
somaticseq/utilities/trimSoftClippedReads.py
somaticseq/utilities/variant_annotation.py
somaticseq/utilities/vcfsorter.pl
somaticseq/utilities/dockered_pipelines/__init__.py
somaticseq/utilities/dockered_pipelines/container_option.py
somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py
somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py
somaticseq/utilities/dockered_pipelines/run_workflows.py
somaticseq/utilities/dockered_pipelines/tumor_normal_run.py
somaticseq/utilities/dockered_pipelines/tumor_only_run.py
somaticseq/utilities/dockered_pipelines/alignments/__init__.py
somaticseq/utilities/dockered_pipelines/alignments/align.py
somaticseq/utilities/dockered_pipelines/alignments/markdup.py
somaticseq/utilities/dockered_pipelines/alignments/mergeBams.py
somaticseq/utilities/dockered_pipelines/alignments/mergeFastqs.py
somaticseq/utilities/dockered_pipelines/alignments/spreadFastq.py
somaticseq/utilities/dockered_pipelines/alignments/trim.py
somaticseq/utilities/dockered_pipelines/somatic_mutations/JointSNVMix2.py
somaticseq/utilities/dockered_pipelines/somatic_mutations/LoFreq.py
somaticseq/utilities/dockered_pipelines/somatic_mutations/MuSE.py
somaticseq/utilities/dockered_pipelines/somatic_mutations/MuTect2.py
somaticseq/utilities/dockered_pipelines/somatic_mutations/Scalpel.py
somaticseq/utilities/dockered_pipelines/somatic_mutations/SomaticSniper.py
somaticseq/utilities/dockered_pipelines/somatic_mutations/Strelka2.py
somaticseq/utilities/dockered_pipelines/somatic_mutations/VarDict.py
somaticseq/utilities/dockered_pipelines/somatic_mutations/VarScan2.py
somaticseq/utilities/dockered_pipelines/somatic_mutations/__init__.py
somaticseq/vcfModifier/__init__.py
somaticseq/vcfModifier/complex2indel.py
somaticseq/vcfModifier/copy_TextFile.py
somaticseq/vcfModifier/getUniqueVcfPositions.py
somaticseq/vcfModifier/leftAlign.py
somaticseq/vcfModifier/modify_JointSNVMix2.py
somaticseq/vcfModifier/modify_MuTect.py
somaticseq/vcfModifier/modify_MuTect2.py
somaticseq/vcfModifier/modify_SomaticSniper.py
somaticseq/vcfModifier/modify_Strelka.py
somaticseq/vcfModifier/modify_VarDict.py
somaticseq/vcfModifier/modify_VarScan2.py
somaticseq/vcfModifier/modify_ssMuTect2.py
somaticseq/vcfModifier/modify_ssStrelka.py
somaticseq/vcfModifier/splitVcf.py
somaticseq/vcfModifier/vcfIntersector.py