Files in TearsWillFall/ULPwgs

An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Graph.pdf R/aasuite.R R/analysis.R R/ascat.R R/batch_constructor.R R/bcftools.R R/bed.R R/build_shiny.R R/bwa.R R/circlemap.R R/ciri.R R/cnvkit.R R/config.R R/coverage.R R/data.R R/dilutions.R R/fasta.R R/fastqc.R R/fragments.R R/gatk.R R/gpos.R R/hatchet.R R/hmmutils.R R/htslib.R R/ichorcna.R R/ichorcna_plot.R R/ichorcna_seg.R R/ichorcna_util.R R/install_required_tools.R R/manta.R R/meddic2.R R/nextflow.R R/other_code.R R/phasing.R R/picard.R R/pileup.R R/ploidy.R R/plots.R R/preprocess.R R/refphase.R R/samtools.R R/shapeit.R R/skewer.R R/strelka.R R/tables.R R/trento.R R/ucsc.R R/util.R R/utils-pipe.R R/vcf.R R/vep.R README.md inst/R/get_tf_from_cnvkit.R man/aa_nextflow.Rd man/access_cnvkit.Rd man/add_af_strelka_vcf.Rd man/add_gl_af_strelka_vcf.Rd man/add_indel_af_strelka_vcf.Rd man/add_snv_af_strelka_vcf.Rd man/add_sv_af_strelka_vcf.Rd man/alignment_bwa.Rd man/analyze_covariates_gatk.Rd man/annotate_bed_circlemap.Rd man/annotate_germline_output_strelka.Rd man/annotate_output_manta.Rd man/annotate_somatic_output_strelka.Rd man/annotate_strelka_vep.Rd man/annotate_vep.Rd man/append_env.Rd man/apply_BQSR_gatk.Rd man/autobin_cnvkit.Rd man/await_scheduler.Rd man/bed_coverage.Rd man/bigBedToBed_ucsc.Rd man/bin_chromosomes.Rd man/bin_genome.Rd man/bin_targets_cnvkit.Rd man/build_default_binary_list.Rd man/build_default_cache_list.Rd man/build_default_chr_list.Rd man/build_default_clonet_dir_list.Rd man/build_default_cn_list.Rd man/build_default_config.Rd man/build_default_hatchet_config.Rd man/build_default_license_list.Rd man/build_default_myriad_module_list.Rd man/build_default_nf_list.Rd man/build_default_option_list.Rd man/build_default_parameter_list.Rd man/build_default_preprocess_config.Rd man/build_default_python_enviroment_list.Rd man/build_default_reference_list.Rd man/build_default_sample_sheet.Rd man/build_default_sif_list.Rd man/build_default_steps_list.Rd man/build_default_tool_binary_list.Rd man/build_default_variable_list.Rd man/build_flowcell_id.Rd man/build_instrument_id.Rd man/build_job.Rd man/build_job_report.Rd man/build_step.Rd man/call_aasuite.Rd man/call_ascat.Rd man/call_coverage_cnvkit.Rd man/call_germline_snvs_strelka.Rd man/call_germline_sv_manta.Rd man/call_get_insert_size_samtools.Rd man/call_haplotypecaller_gatk.Rd man/call_refphase.Rd man/call_snvs_strelka.Rd man/call_somatic_snvs_strelka.Rd man/call_somatic_sv_manta.Rd man/call_sv_manta.Rd man/call_variants_strelka.Rd man/check_if_compressed.Rd man/check_job_limit.Rd man/check_missing.Rd man/check_pcf_identity.Rd man/check_req_cols.Rd man/check_req_types.Rd man/circ_quant_rna.Rd man/circ_rna.Rd man/circdna_circlemap.Rd man/clonet_trento.Rd man/clonet_view_trento.Rd man/cnn_score_variants_gatk.Rd man/complement_bed.Rd man/compress_and_index_bed_htslib.Rd man/compress_and_index_vcf_htslib.Rd man/compress_bed_htslib.Rd man/compress_vcf_htslib.Rd man/concat_file_list.Rd man/concat_vcf.Rd man/concatenate_bams.Rd man/correctLog2_ascat.Rd man/coverage_cnvkit.Rd man/cp_data.Rd man/create_antitarget_cnvkit.Rd man/create_genomic_db_gatk.Rd man/create_pon_cnvkit.Rd man/create_pon_gatk.Rd man/create_target_cnvkit.Rd man/diagram_cnvkit.Rd man/estimate_contamination_gatk.Rd man/evaluate_tf.Rd man/extract_body_vcf.Rd man/extract_csq_info_vcf.Rd man/extract_descriptors_vcf.Rd man/extract_pass_variants_strelka_vcf.Rd man/extract_read_header.Rd man/file_cp.Rd man/file_rm.Rd man/file_scp.Rd man/filter_bam.Rd man/filter_bam_by_size_samtools.Rd man/filter_chr.Rd man/filter_tabulated_vcf.Rd man/filter_variant_tranches_gatk.Rd man/find_instrument.Rd man/fix_cnvkit.Rd man/for_id.Rd man/gather_BQSR_reports_gatk.Rd man/gather_bam_files_picard.Rd man/generate_BQSR_gatk.Rd man/get_bam_reference_chr.Rd man/get_base_fasta.Rd man/get_coverage.Rd man/get_coverage_tfbs.Rd man/get_fai_reference_chr.Rd man/get_file_ext.Rd man/get_file_name.Rd man/get_insert_size_samtools.Rd man/get_sq_bam.Rd man/get_tf_from_cnvkit.Rd man/get_tf_from_sample.Rd man/haplotypecaller_gatk.Rd man/ichorCNA.Rd man/ichor_capture.Rd man/ichor_wgs.Rd man/index_bam_samtools.Rd man/index_bed_htslib.Rd man/index_ref_bwa.Rd man/index_vcf_htslib.Rd man/infer_sequencing_info.Rd man/insertsize_metrics_bam_picard.Rd man/install_required_tools.Rd man/intersect_file_name.Rd man/job_validator.Rd man/learn_orientation_gatk.Rd man/liftOver_ucsc.Rd man/ln_data.Rd man/make_unique_id.Rd man/mapq_metrics_bam_samtools.Rd man/markdups_gatk.Rd man/markdups_picard.Rd man/mclapply_os.Rd man/merge_bams_samtools.Rd man/merge_mutect_stats_gatk.Rd man/metrics_alignqc.Rd man/mpileup_samtools.Rd man/multisample_clonet_trento.Rd man/multisample_mutect2_gatk.Rd man/mutect2_gatk.Rd man/mutect_filter_gatk.Rd man/myriad_module.Rd man/nest_vcf_body.Rd man/new_clonet_trento.Rd man/new_flag_stats_samtools.Rd man/new_get_insert_size_samtools.Rd man/new_haplotypecaller_gatk.Rd man/new_index_bam_samtools.Rd man/new_index_stats_samtools.Rd man/new_insertsize_metrics_bam_picard.Rd man/new_sort_and_index_bam_samtools.Rd man/new_sort_bam_samtools.Rd man/new_stats_bam_samtools.Rd man/new_tg_summary_metrics_bam_picard.Rd man/pad_bed.Rd man/panel_of_normals_ichorCNA.Rd man/parallel_apply_BQSR_gatk.Rd man/parallel_estimate_contamination_gatk.Rd man/parallel_generate_BQSR_gatk.Rd man/parallel_pileup_summary_gatk.Rd man/parallel_region_filter_bam_by_size_samtools.Rd man/parallel_region_get_insert_size_samtools.Rd man/parallel_regions_mutect2_gatk.Rd man/parallel_sample_bigBedToBed_ucsc.Rd man/parallel_sample_ichor_capture.Rd man/parallel_samples_call_ascat.Rd man/parallel_samples_mutect2_gatk.Rd man/parameter_config_check.Rd man/parse_args.Rd man/parse_picard_metrics.Rd man/parse_read_header.Rd man/parse_summary_picard.Rd man/parse_tool_parameters.Rd man/phase_chr_shapeit.Rd man/phase_shapeit.Rd man/pileup_summary_gatk.Rd man/pipe.Rd man/ploidy_from_cnr.Rd man/ploidy_from_cns.Rd man/plot_cnvkit.Rd man/plot_coverage_panel.Rd man/plot_cumulative_cov.Rd man/prepare_ascat.Rd man/preprocess_seq.Rd man/preprocess_seq_trento.Rd man/process_ascat.Rd man/process_cnvkit.Rd man/process_refphase.Rd man/process_sample.Rd man/qc_fastqc.Rd man/qdel.Rd man/qstat.Rd man/read_and_load_ascat_refphase.Rd man/read_bed.Rd man/read_bed_circlemap.Rd man/read_counter.Rd man/read_counter_region.Rd man/read_extractor_circlemap.Rd man/read_fai.Rd man/read_fasta.Rd man/read_gpos.Rd man/read_job_report.Rd man/read_pileup.Rd man/read_vcf.Rd man/realign_circlemap.Rd man/recal_gatk.Rd man/reference_cnvkit.Rd man/repeat_caller_circlemap.Rd man/replace_rg.Rd man/rnaseq_summary_metrics_bam_picard.Rd man/run_hatchet.Rd man/run_meddic2.Rd man/sample_bam_samtools.Rd man/scatter_cnvkit.Rd man/segment_cnvkit.Rd man/seq_info_check.Rd man/seqlast.Rd man/set_dir.Rd man/set_input_id.Rd man/set_inputs.Rd man/set_name.Rd man/sliding_bin_genome.Rd man/sort_and_index_bam_samtools.Rd man/sort_bam_samtools.Rd man/sort_vcf.Rd man/stats_bam_samtools.Rd man/stats_flag_samtools.Rd man/stats_index_samtools.Rd man/summary_metrics_bam_picard.Rd man/tabulate_info_vcf.Rd man/tabulate_vcf.Rd man/tg_summary_metrics_bam_picard.Rd man/thisFile.Rd man/trimming_skewer.Rd man/uncompress_bed_htslib.Rd man/uncompress_vcf_htslib.Rd man/unnest_vcf_body.Rd man/untabulate_info_vcf.Rd man/validate_arg.Rd man/validate_input_args.Rd man/validate_sample_sheet.Rd man/variants_by_filters_vcf.Rd man/variants_by_type_vcf.Rd man/wgs_summary_metrics_bam_picard.Rd man/with_env.Rd man/write_vcf.Rd test.R