├── .gitignore ├── Dockerfiles ├── akt.0.3.2.dockerfile ├── alientrimmer.0.4.0.dockerfile ├── bwa.0.7.17_samtools.dockerfile ├── canvas.1.35.dockerfile ├── jsm.0.7.5-1.dockerfile ├── lofreq.2.1.3.1-1.dockerfile ├── manta.1.4.0.dockerfile ├── muse_1.0rc_c.dockerfile ├── nirvana.2.0.9.dockerfile ├── picard.2.27.5.dockerfile ├── sambamba.1.0.0.dockerfile ├── samtools.1.19.2.dockerfile ├── scalpel.0.5.4.dockerfile ├── somaticseq.base-1.7.dockerfile ├── somaticseq.master.dockerfile ├── somaticseq.release.dockerfile ├── somaticsniper.1.0.5.0-2.dockerfile ├── strelka.2.9.5.dockerfile ├── tabix.1.19.dockerfile ├── trimmomatic.0.39.dockerfile ├── vardictjava.dockerfile └── vcftools.0.1.14-2.dockerfile ├── LICENSE.txt ├── MODULES.md ├── README.md ├── docs ├── Manual.pdf ├── Manual.tex ├── Manual.tex.backup ├── Refs.bib ├── SomaticSeqYoutube.png ├── heatmap400.png ├── precisionfda.png ├── seqc2.md ├── train_for_classifiers.md └── workflow400.png ├── pyproject.toml ├── r_scripts ├── __init__.py ├── ada_cross_validation.R ├── ada_model_builder.R ├── ada_model_builder_ntChange.R └── ada_model_predictor.R ├── setup.cfg ├── setup.py ├── somaticseq ├── __init__.py ├── _version.py ├── annotate_caller.py ├── bam_features.py ├── combine_callers.py ├── defaults.py ├── genomic_file_parsers │ ├── __init__.py │ ├── concat.py │ ├── genomic_file_handlers.py │ ├── pileup_reader.py │ └── read_info_extractor.py ├── ntchange_type.py ├── run_somaticseq.py ├── sequencing_features.py ├── single_sample_vcf2tsv.py ├── somatic_tsv2vcf.py ├── somatic_vcf2tsv.py ├── somatic_xgboost.py ├── somaticseq_parallel.py ├── tsv2vcf.py ├── utilities │ ├── BAM_filter.py │ ├── README.md │ ├── __init__.py │ ├── attach_pileupVAF.py │ ├── bamQC.py │ ├── bedFileHandler.py │ ├── combo_callers_evaluator.py │ ├── dockered_pipelines │ │ ├── QC │ │ │ ├── extract_callableRegions.sh │ │ │ └── extract_coverageDepth.sh │ │ ├── README.md │ │ ├── __init__.py │ │ ├── alignments │ │ │ ├── BQSR.sh │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── align.py │ │ │ ├── jointIndelRealign.sh │ │ │ ├── markdup.py │ │ │ ├── mergeBams.py │ │ │ ├── mergeFastqs.py │ │ │ ├── singleIndelRealign.sh │ │ │ ├── spreadFastq.py │ │ │ └── trim.py │ │ ├── bamSimulator │ │ │ ├── BamSimulator_multiThreads.sh │ │ │ ├── BamSimulator_singleThread.sh │ │ │ ├── README.md │ │ │ ├── bamSurgeon │ │ │ │ ├── IndelRealign.sh │ │ │ │ ├── MergeTN.sh │ │ │ │ ├── Reheader_SM.sh │ │ │ │ ├── SortByCoordinate.sh │ │ │ │ ├── SortByReadName.sh │ │ │ │ ├── bamsurgeon_addindels.sh │ │ │ │ ├── bamsurgeon_addsnvs.sh │ │ │ │ ├── bamsurgeon_addsvs.sh │ │ │ │ ├── bamsurgeon_random_sites.sh │ │ │ │ ├── bamsurgeon_split_BAM.sh │ │ │ │ ├── cleanBam.sh │ │ │ │ ├── concatVcfFiles.sh │ │ │ │ ├── convert_nonStandardBasesInVcfs.py │ │ │ │ ├── mergeBamFiles.sh │ │ │ │ └── split_BAM_by_BED.sh │ │ │ ├── dream_sim.jpg │ │ │ ├── onkoinsight_sim.png │ │ │ └── replicate_sim.jpg │ │ ├── container_option.py │ │ ├── germline_variants │ │ │ ├── Canvas.sh │ │ │ ├── Manta.sh │ │ │ ├── Nirvana.sh │ │ │ ├── README.md │ │ │ ├── VQSR.sh │ │ │ ├── bam2vcf.sh │ │ │ └── haplotypeCaller.sh │ │ ├── makeAlignmentScripts.py │ │ ├── makeSomaticScripts.py │ │ ├── run_workflows.py │ │ ├── somatic_mutations │ │ │ ├── JointSNVMix2.py │ │ │ ├── LoFreq.py │ │ │ ├── MuSE.py │ │ │ ├── MuTect2.py │ │ │ ├── Scalpel.py │ │ │ ├── SomaticSniper.py │ │ │ ├── Strelka2.py │ │ │ ├── VarDict.py │ │ │ ├── VarScan2.py │ │ │ └── __init__.py │ │ ├── tumor_normal_run.py │ │ └── tumor_only_run.py │ ├── filter_SomaticSeq_VCF.py │ ├── linguistic_sequence_complexity.py │ ├── lociCounterWithLabels.py │ ├── lociCounters.py │ ├── multi-nucleotide_phaser.py │ ├── paired_end_bam2fastq.py │ ├── plot_TPvsFP.py │ ├── reformat_VCF2SEQC2.py │ ├── remove_callers_from_somaticseq_tsv.py │ ├── singularities │ │ ├── QC │ │ │ ├── extract_callableRegions.sh │ │ │ └── extract_coverageDepth.sh │ │ ├── README.md │ │ ├── bamSimulator │ │ │ ├── BamSimulator_multiThreads.sh │ │ │ ├── BamSimulator_singleThread.sh │ │ │ ├── README.md │ │ │ └── bamSurgeon │ │ │ │ ├── IndelRealign.sh │ │ │ │ ├── MergeTN.sh │ │ │ │ ├── Reheader_SM.sh │ │ │ │ ├── SortByCoordinate.sh │ │ │ │ ├── SortByReadName.sh │ │ │ │ ├── bamsurgeon_addindels.sh │ │ │ │ ├── bamsurgeon_addsnvs.sh │ │ │ │ ├── bamsurgeon_addsvs.sh │ │ │ │ ├── bamsurgeon_random_sites.sh │ │ │ │ ├── bamsurgeon_split_BAM.sh │ │ │ │ ├── cleanBam.sh │ │ │ │ ├── concatVcfFiles.sh │ │ │ │ ├── mergeBamFiles.sh │ │ │ │ └── split_BAM_by_BED.sh │ │ └── germline_variants │ │ │ ├── Nirvana.sh │ │ │ ├── VQSR.sh │ │ │ ├── bam2vcf.sh │ │ │ └── haplotypeCaller.sh │ ├── snakemake │ │ ├── README.md │ │ ├── Snakefile │ │ └── config.yaml │ ├── split_bed_into_equal_regions.py │ ├── split_mergedBed.py │ ├── tally_MyVCF_vs_Truth.py │ ├── tally_variants_from_multiple_vcfs.py │ ├── trimSoftClippedReads.py │ ├── variant_annotation.py │ └── vcfsorter.pl └── vcf_modifier │ ├── __init__.py │ ├── bed_util.py │ ├── complex2indel.py │ ├── copy_TextFile.py │ ├── getUniqueVcfPositions.py │ ├── leftAlign.py │ ├── modify_JointSNVMix2.py │ ├── modify_MuTect.py │ ├── modify_MuTect2.py │ ├── modify_SomaticSniper.py │ ├── modify_Strelka.py │ ├── modify_VarDict.py │ ├── modify_VarScan2.py │ ├── modify_ssMuTect2.py │ ├── modify_ssStrelka.py │ └── split_vcf.py ├── tests ├── conftest.py ├── example │ ├── README.md │ ├── Varsim.somatic.truth.vcf │ ├── invoke_dockerized_tumor_normal_callers.sh │ ├── invoke_dockerized_tumor_only_callers.sh │ ├── normal.markdup.bam │ ├── normal.markdup.bam.bai │ ├── paired_example │ │ ├── Consensus.sINDEL.vcf.gz │ │ ├── Consensus.sSNV.vcf.gz │ │ ├── LoFreq.indel.vcf.gz │ │ ├── LoFreq.snv.vcf.gz │ │ ├── MuSE.vcf.gz │ │ ├── MuTect2.vcf.gz │ │ ├── Scalpel.vcf.gz │ │ ├── SomaticSniper.vcf.gz │ │ ├── Strelka.indel.vcf.gz │ │ ├── Strelka.snv.vcf.gz │ │ └── VarDict.vcf.gz │ ├── paired_somaticseq_example.sh │ ├── results_check.sh │ ├── single_somaticseq_example.sh │ ├── tiny.dict │ ├── tiny.fa │ ├── tiny.fa.fai │ ├── tiny_dbsnp.vcf │ ├── tiny_dbsnp.vcf.gz │ 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