python-scripts/ada_model_builder_ntChange.R
python-scripts/ada_model_predictor.R
python-scripts/concat.py
python-scripts/linguistic_sequence_complexity.py
python-scripts/lociCounterWithLabels.py
python-scripts/makeAlignmentScripts.py
python-scripts/makeSomaticScripts.py
python-scripts/paired_end_bam2fastq.py
python-scripts/remove_callers_from_somaticseq_tsv.py
python-scripts/run_somaticseq.py
python-scripts/run_workflows.py
python-scripts/single_sample_vcf2tsv.py
python-scripts/somatic_tsv2vcf.py
python-scripts/somatic_vcf2tsv.py
python-scripts/somatic_xgboost.py
python-scripts/somaticseq_parallel.py
python-scripts/split_bed_into_equal_regions.py
python-scripts/split_vcf.py
python-scripts/tally_variants_from_multiple_vcfs.py
python-scripts/variant_annotation.py
python-scripts/vcfsorter.pl
site-packages/r_scripts/__init__.py
site-packages/r_scripts/ada_cross_validation.R
site-packages/r_scripts/ada_model_builder.R
site-packages/r_scripts/ada_model_builder_ntChange.R
site-packages/r_scripts/ada_model_predictor.R
site-packages/somaticseq-3.12.0.dist-info/INSTALLER
site-packages/somaticseq-3.12.0.dist-info/METADATA
site-packages/somaticseq-3.12.0.dist-info/RECORD
site-packages/somaticseq-3.12.0.dist-info/REQUESTED
site-packages/somaticseq-3.12.0.dist-info/WHEEL
site-packages/somaticseq-3.12.0.dist-info/direct_url.json
site-packages/somaticseq-3.12.0.dist-info/entry_points.txt
site-packages/somaticseq-3.12.0.dist-info/licenses/LICENSE.txt
site-packages/somaticseq-3.12.0.dist-info/top_level.txt
site-packages/somaticseq/__init__.py
site-packages/somaticseq/_version.py
site-packages/somaticseq/annotate_caller.py
site-packages/somaticseq/bam_features.py
site-packages/somaticseq/combine_callers.py
site-packages/somaticseq/defaults.py
site-packages/somaticseq/genomic_file_parsers/__init__.py
site-packages/somaticseq/genomic_file_parsers/concat.py
site-packages/somaticseq/genomic_file_parsers/genomic_file_handlers.py
site-packages/somaticseq/genomic_file_parsers/pileup_reader.py
site-packages/somaticseq/genomic_file_parsers/read_info_extractor.py
site-packages/somaticseq/ntchange_type.py
site-packages/somaticseq/run_somaticseq.py
site-packages/somaticseq/sequencing_features.py
site-packages/somaticseq/single_sample_vcf2tsv.py
site-packages/somaticseq/somatic_tsv2vcf.py
site-packages/somaticseq/somatic_vcf2tsv.py
site-packages/somaticseq/somatic_xgboost.py
site-packages/somaticseq/somaticseq_parallel.py
site-packages/somaticseq/tsv2vcf.py
site-packages/somaticseq/utilities/BAM_filter.py
site-packages/somaticseq/utilities/__init__.py
site-packages/somaticseq/utilities/attach_pileupVAF.py
site-packages/somaticseq/utilities/bamQC.py
site-packages/somaticseq/utilities/bedFileHandler.py
site-packages/somaticseq/utilities/combo_callers_evaluator.py
site-packages/somaticseq/utilities/dockered_pipelines/__init__.py
site-packages/somaticseq/utilities/dockered_pipelines/alignments/__init__.py
site-packages/somaticseq/utilities/dockered_pipelines/alignments/align.py
site-packages/somaticseq/utilities/dockered_pipelines/alignments/markdup.py
site-packages/somaticseq/utilities/dockered_pipelines/alignments/mergeBams.py
site-packages/somaticseq/utilities/dockered_pipelines/alignments/mergeFastqs.py
site-packages/somaticseq/utilities/dockered_pipelines/alignments/spreadFastq.py
site-packages/somaticseq/utilities/dockered_pipelines/alignments/trim.py
site-packages/somaticseq/utilities/dockered_pipelines/container_option.py
site-packages/somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py
site-packages/somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py
site-packages/somaticseq/utilities/dockered_pipelines/run_workflows.py
site-packages/somaticseq/utilities/dockered_pipelines/somatic_mutations/JointSNVMix2.py
site-packages/somaticseq/utilities/dockered_pipelines/somatic_mutations/LoFreq.py
site-packages/somaticseq/utilities/dockered_pipelines/somatic_mutations/MuSE.py
site-packages/somaticseq/utilities/dockered_pipelines/somatic_mutations/MuTect2.py
site-packages/somaticseq/utilities/dockered_pipelines/somatic_mutations/Scalpel.py
site-packages/somaticseq/utilities/dockered_pipelines/somatic_mutations/SomaticSniper.py
site-packages/somaticseq/utilities/dockered_pipelines/somatic_mutations/Strelka2.py
site-packages/somaticseq/utilities/dockered_pipelines/somatic_mutations/VarDict.py
site-packages/somaticseq/utilities/dockered_pipelines/somatic_mutations/VarScan2.py
site-packages/somaticseq/utilities/dockered_pipelines/somatic_mutations/__init__.py
site-packages/somaticseq/utilities/dockered_pipelines/tumor_normal_run.py
site-packages/somaticseq/utilities/dockered_pipelines/tumor_only_run.py
site-packages/somaticseq/utilities/filter_SomaticSeq_VCF.py
site-packages/somaticseq/utilities/linguistic_sequence_complexity.py
site-packages/somaticseq/utilities/lociCounterWithLabels.py
site-packages/somaticseq/utilities/lociCounters.py
site-packages/somaticseq/utilities/multi-nucleotide_phaser.py
site-packages/somaticseq/utilities/paired_end_bam2fastq.py
site-packages/somaticseq/utilities/plot_TPvsFP.py
site-packages/somaticseq/utilities/reformat_VCF2SEQC2.py
site-packages/somaticseq/utilities/remove_callers_from_somaticseq_tsv.py
site-packages/somaticseq/utilities/split_bed_into_equal_regions.py
site-packages/somaticseq/utilities/split_mergedBed.py
site-packages/somaticseq/utilities/tally_MyVCF_vs_Truth.py
site-packages/somaticseq/utilities/tally_variants_from_multiple_vcfs.py
site-packages/somaticseq/utilities/trimSoftClippedReads.py
site-packages/somaticseq/utilities/variant_annotation.py
site-packages/somaticseq/vcf_modifier/__init__.py
site-packages/somaticseq/vcf_modifier/bed_util.py
site-packages/somaticseq/vcf_modifier/complex2indel.py
site-packages/somaticseq/vcf_modifier/copy_TextFile.py
site-packages/somaticseq/vcf_modifier/getUniqueVcfPositions.py
site-packages/somaticseq/vcf_modifier/leftAlign.py
site-packages/somaticseq/vcf_modifier/modify_JointSNVMix2.py
site-packages/somaticseq/vcf_modifier/modify_MuTect.py
site-packages/somaticseq/vcf_modifier/modify_MuTect2.py
site-packages/somaticseq/vcf_modifier/modify_SomaticSniper.py
site-packages/somaticseq/vcf_modifier/modify_Strelka.py
site-packages/somaticseq/vcf_modifier/modify_VarDict.py
site-packages/somaticseq/vcf_modifier/modify_VarScan2.py
site-packages/somaticseq/vcf_modifier/modify_ssMuTect2.py
site-packages/somaticseq/vcf_modifier/modify_ssStrelka.py
site-packages/somaticseq/vcf_modifier/split_vcf.py
