├── .gitignore ├── README.md ├── bin ├── digest_calls.R ├── scan2 └── scan2_download_eagle_refpanel.sh ├── enrichment ├── bedenrich.r ├── enrichment.r └── inoutenrich.r ├── recipes ├── build_command.sh └── scan2 │ ├── build.sh │ ├── info │ └── has_prefix │ └── meta.yaml ├── resources ├── analysis_regions │ └── analysis_regions_file_hs37d5.txt └── binned_counts │ ├── hg38 │ ├── bins_mapq60_width1000.bed.gz │ ├── gc_content.tab.gz │ └── gc_content.tab.gz.tbi │ └── hs37d5 │ ├── bins_mapq60_width1000.bed.gz │ ├── gc_content.tab.gz │ └── gc_content.tab.gz.tbi ├── scripts ├── call_mutations.R ├── collect_benchmarks.sh ├── combine_permutations.R ├── compute_ab_ests_and_models.R ├── compute_excess_cigar_scores.R ├── concat_tabix.sh ├── count_cigars.py ├── digest_depth.R ├── expand_analysis_regions.sh ├── gatk_doc_to_bed.sh ├── gen_version.sh ├── integrate_tables.R ├── join_phased_hsnps.R ├── joint_depth_matrix_to_bigwig.sh ├── make_callable_regions_bed.R ├── make_panel.R ├── make_permutations.R ├── make_tiny_object.R ├── mutsig_rescue.R ├── pregenotyping.R ├── prepare_ginkgo.sh ├── run_bamtobed.sh ├── run_ginkgo.sh ├── sample_from_bam.sh ├── scan2_to_vcf.R ├── spatial_sens_depth.R ├── spatial_sens_integrate.R ├── summarize_depth_gather.R ├── summarize_depth_scatter.awk ├── summarize_object.R ├── totab.depth_profile.sh ├── totab.panel.sh ├── totab.phase.sh └── totab.sh └── snakemake ├── Snakefile ├── scripts ├── abmodel_covariates.R ├── abmodel_fit_script.R ├── abmodel_gather_by_chrom_script.R ├── abmodel_gather_tiled_script.R ├── abmodel_gradient_gather.R ├── abmodel_gradient_scatter.R ├── abmodel_scatter_chrom_tiled_script.R ├── abmodel_scatter_script.R ├── callable_regions_gather_script.R ├── callable_regions_summarize_script.R ├── scansnv_cigar_gather_script.R ├── scansnv_cigar_scores_gather_script.R ├── scansnv_cigar_scores_scatter_script.R ├── scansnv_cigar_tuning_script.R ├── scansnv_genotype_gather_script.R ├── scansnv_genotype_gather_script_object.R ├── scansnv_genotype_mosaic_gather_script.R ├── scansnv_indel_pon_script.R ├── scansnv_mosaic_sites_script.R ├── scansnv_sample_hsnps_script.R ├── scansnv_somatic_sites_script.R ├── scansnv_somatic_sites_script_allsites.R ├── training_hsnps_adjust_phase_script.R ├── training_hsnps_script.R └── training_indels_script.R ├── snakefile.abmodel ├── snakefile.call_mutations ├── snakefile.cigars ├── snakefile.depth_profile ├── snakefile.gatk3_joint ├── snakefile.gatk4_gvcf ├── snakefile.gatk4_joint ├── snakefile.gatk_shared ├── snakefile.gatk_user_vcf ├── snakefile.genotype ├── snakefile.integrated_table ├── snakefile.makepanel ├── snakefile.permtool ├── snakefile.phasing_eagle ├── snakefile.phasing_shapeit ├── snakefile.phasing_shared ├── snakefile.rescue ├── snakefile.select_gatk ├── snakefile.select_phaser ├── snakefile.sensitivity ├── snakefile.sentieon_gvcf ├── snakefile.sentieon_joint └── snakefile.user_supplied_phasing /.gitignore: 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