.gitignore
LICENSE.txt
MODULES.md
README.md
pyproject.toml
setup.cfg
setup.py
Dockerfiles/akt.0.3.2.dockerfile
Dockerfiles/alientrimmer.0.4.0.dockerfile
Dockerfiles/bwa.0.7.17_samtools.dockerfile
Dockerfiles/canvas.1.35.dockerfile
Dockerfiles/jsm.0.7.5-1.dockerfile
Dockerfiles/lofreq.2.1.3.1-1.dockerfile
Dockerfiles/manta.1.4.0.dockerfile
Dockerfiles/muse_1.0rc_c.dockerfile
Dockerfiles/nirvana.2.0.9.dockerfile
Dockerfiles/picard.2.27.5.dockerfile
Dockerfiles/sambamba.1.0.0.dockerfile
Dockerfiles/samtools.1.19.2.dockerfile
Dockerfiles/scalpel.0.5.4.dockerfile
Dockerfiles/somaticseq.master.dockerfile
Dockerfiles/somaticsniper.1.0.5.0-2.dockerfile
Dockerfiles/strelka.2.9.5.dockerfile
Dockerfiles/tabix.1.19.dockerfile
Dockerfiles/trimmomatic.0.39.dockerfile
Dockerfiles/vardictjava.dockerfile
Dockerfiles/vcftools.0.1.14-2.dockerfile
docs/Manual.pdf
docs/Manual.tex
docs/Manual.tex.backup
docs/Refs.bib
docs/SomaticSeqYoutube.png
docs/heatmap400.png
docs/precisionfda.png
docs/seqc2.md
docs/train_for_classifiers.md
docs/workflow400.png
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
somaticseq/__init__.py
somaticseq/_version.py
somaticseq/annotate_caller.py
somaticseq/bam_features.py
somaticseq/combine_callers.py
somaticseq/defaults.py
somaticseq/ntchange_type.py
somaticseq/run_somaticseq.py
somaticseq/sequencing_features.py
somaticseq/single_sample_vcf2tsv.py
somaticseq/somatic_tsv2vcf.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/entry_points.txt
somaticseq.egg-info/requires.txt
somaticseq.egg-info/top_level.txt
somaticseq/genomic_file_parsers/__init__.py
somaticseq/genomic_file_parsers/concat.py
somaticseq/genomic_file_parsers/genomic_file_handlers.py
somaticseq/genomic_file_parsers/pileup_reader.py
somaticseq/genomic_file_parsers/read_info_extractor.py
somaticseq/utilities/BAM_filter.py
somaticseq/utilities/README.md
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/README.md
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/QC/extract_callableRegions.sh
somaticseq/utilities/dockered_pipelines/QC/extract_coverageDepth.sh
somaticseq/utilities/dockered_pipelines/alignments/BQSR.sh
somaticseq/utilities/dockered_pipelines/alignments/README.md
somaticseq/utilities/dockered_pipelines/alignments/__init__.py
somaticseq/utilities/dockered_pipelines/alignments/align.py
somaticseq/utilities/dockered_pipelines/alignments/jointIndelRealign.sh
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/singleIndelRealign.sh
somaticseq/utilities/dockered_pipelines/alignments/spreadFastq.py
somaticseq/utilities/dockered_pipelines/alignments/trim.py
somaticseq/utilities/dockered_pipelines/bamSimulator/BamSimulator_multiThreads.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/BamSimulator_singleThread.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/README.md
somaticseq/utilities/dockered_pipelines/bamSimulator/dream_sim.jpg
somaticseq/utilities/dockered_pipelines/bamSimulator/onkoinsight_sim.png
somaticseq/utilities/dockered_pipelines/bamSimulator/replicate_sim.jpg
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/IndelRealign.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/MergeTN.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/Reheader_SM.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/SortByCoordinate.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/SortByReadName.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/bamsurgeon_addindels.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/bamsurgeon_addsnvs.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/bamsurgeon_addsvs.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/bamsurgeon_random_sites.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/bamsurgeon_split_BAM.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/cleanBam.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/concatVcfFiles.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/convert_nonStandardBasesInVcfs.py
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/mergeBamFiles.sh
somaticseq/utilities/dockered_pipelines/bamSimulator/bamSurgeon/split_BAM_by_BED.sh
somaticseq/utilities/dockered_pipelines/germline_variants/Canvas.sh
somaticseq/utilities/dockered_pipelines/germline_variants/Manta.sh
somaticseq/utilities/dockered_pipelines/germline_variants/Nirvana.sh
somaticseq/utilities/dockered_pipelines/germline_variants/README.md
somaticseq/utilities/dockered_pipelines/germline_variants/VQSR.sh
somaticseq/utilities/dockered_pipelines/germline_variants/bam2vcf.sh
somaticseq/utilities/dockered_pipelines/germline_variants/haplotypeCaller.sh
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/utilities/singularities/README.md
somaticseq/utilities/singularities/QC/extract_callableRegions.sh
somaticseq/utilities/singularities/QC/extract_coverageDepth.sh
somaticseq/utilities/singularities/bamSimulator/BamSimulator_multiThreads.sh
somaticseq/utilities/singularities/bamSimulator/BamSimulator_singleThread.sh
somaticseq/utilities/singularities/bamSimulator/README.md
somaticseq/utilities/singularities/bamSimulator/bamSurgeon/IndelRealign.sh
somaticseq/utilities/singularities/bamSimulator/bamSurgeon/MergeTN.sh
somaticseq/utilities/singularities/bamSimulator/bamSurgeon/Reheader_SM.sh
somaticseq/utilities/singularities/bamSimulator/bamSurgeon/SortByCoordinate.sh
somaticseq/utilities/singularities/bamSimulator/bamSurgeon/SortByReadName.sh
somaticseq/utilities/singularities/bamSimulator/bamSurgeon/bamsurgeon_addindels.sh
somaticseq/utilities/singularities/bamSimulator/bamSurgeon/bamsurgeon_addsnvs.sh
somaticseq/utilities/singularities/bamSimulator/bamSurgeon/bamsurgeon_addsvs.sh
somaticseq/utilities/singularities/bamSimulator/bamSurgeon/bamsurgeon_random_sites.sh
somaticseq/utilities/singularities/bamSimulator/bamSurgeon/bamsurgeon_split_BAM.sh
somaticseq/utilities/singularities/bamSimulator/bamSurgeon/cleanBam.sh
somaticseq/utilities/singularities/bamSimulator/bamSurgeon/concatVcfFiles.sh
somaticseq/utilities/singularities/bamSimulator/bamSurgeon/mergeBamFiles.sh
somaticseq/utilities/singularities/bamSimulator/bamSurgeon/split_BAM_by_BED.sh
somaticseq/utilities/singularities/germline_variants/Nirvana.sh
somaticseq/utilities/singularities/germline_variants/VQSR.sh
somaticseq/utilities/singularities/germline_variants/bam2vcf.sh
somaticseq/utilities/singularities/germline_variants/haplotypeCaller.sh
somaticseq/utilities/snakemake/README.md
somaticseq/utilities/snakemake/Snakefile
somaticseq/utilities/snakemake/config.yaml
somaticseq/vcf_modifier/__init__.py
somaticseq/vcf_modifier/bed_util.py
somaticseq/vcf_modifier/complex2indel.py
somaticseq/vcf_modifier/copy_TextFile.py
somaticseq/vcf_modifier/getUniqueVcfPositions.py
somaticseq/vcf_modifier/leftAlign.py
somaticseq/vcf_modifier/modify_JointSNVMix2.py
somaticseq/vcf_modifier/modify_MuTect.py
somaticseq/vcf_modifier/modify_MuTect2.py
somaticseq/vcf_modifier/modify_SomaticSniper.py
somaticseq/vcf_modifier/modify_Strelka.py
somaticseq/vcf_modifier/modify_VarDict.py
somaticseq/vcf_modifier/modify_VarScan2.py
somaticseq/vcf_modifier/modify_ssMuTect2.py
somaticseq/vcf_modifier/modify_ssStrelka.py
somaticseq/vcf_modifier/split_vcf.py
tests/conftest.py
tests/example/README.md
tests/example/Varsim.somatic.truth.vcf
tests/example/invoke_dockerized_tumor_normal_callers.sh
tests/example/invoke_dockerized_tumor_only_callers.sh
tests/example/normal.markdup.bam
tests/example/normal.markdup.bam.bai
tests/example/paired_somaticseq_example.sh
tests/example/results_check.sh
tests/example/single_somaticseq_example.sh
tests/example/tiny.dict
tests/example/tiny.fa
tests/example/tiny.fa.fai
tests/example/tiny_dbsnp.vcf
tests/example/tiny_dbsnp.vcf.gz
tests/example/tiny_dbsnp.vcf.gz.tbi
tests/example/tumor.markdup.bam
tests/example/tumor.markdup.bam.bai
tests/example/paired_example/Consensus.sINDEL.vcf.gz
tests/example/paired_example/Consensus.sSNV.vcf.gz
tests/example/paired_example/LoFreq.indel.vcf.gz
tests/example/paired_example/LoFreq.snv.vcf.gz
tests/example/paired_example/MuSE.vcf.gz
tests/example/paired_example/MuTect2.vcf.gz
tests/example/paired_example/Scalpel.vcf.gz
tests/example/paired_example/SomaticSniper.vcf.gz
tests/example/paired_example/Strelka.indel.vcf.gz
tests/example/paired_example/Strelka.snv.vcf.gz
tests/example/paired_example/VarDict.vcf.gz
tests/example/tumor_only_example/Consensus.sINDEL.vcf.gz
tests/example/tumor_only_example/Consensus.sSNV.vcf.gz
tests/example/tumor_only_example/MuTect2.vcf.gz
tests/example/tumor_only_example/Strelka.vcf.gz
tests/example/tumor_only_example/VarDict.vcf.gz
tests/functional/test_somaticseq.py
tests/unit/vcf_modifier/test_split_vcf.py