Man pages for 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
| aa_nextflow | Run ampliconArchitect suite on nextflow |
| access_cnvkit | Wrapper around access command in CNVkit |
| add_af_strelka_vcf | Add structural variant AF information to Strelka VCF file... |
| add_gl_af_strelka_vcf | Add structural variant AF information to Strelka VCF file... |
| add_indel_af_strelka_vcf | Add indel AF information to Strelka VCF file This function... |
| add_snv_af_strelka_vcf | Add SNV AF information to Strelka VCF file This function... |
| add_sv_af_strelka_vcf | Add structural variant AF information to Strelka VCF file... |
| alignment_bwa | Read alignment using BWA |
| analyze_covariates_gatk | Wrapper of AnalyzeCovariates function in gatk |
| annotate_bed_circlemap | Annotate Circle-Map circDNA BED file output |
| annotate_germline_output_strelka | Strelka wrapper for germline SNV variant calling |
| annotate_output_manta | Strelka wrapper for germline SNV variant calling |
| annotate_somatic_output_strelka | Strelka wrapper for germline SNV variant calling |
| annotate_strelka_vep | Create Read Orientation Model for Mutect2 Filter |
| annotate_vep | Create Read Orientation Model for Mutect2 Filter |
| append_env | Append two enviroments |
| apply_BQSR_gatk | Wrapper of applyBQSR function gatk |
| autobin_cnvkit | Wrapper around autobin function from CNVkit |
| await_scheduler | Build execution innit for function to execute |
| bed_coverage | Estimate coverage for BED file |
| bigBedToBed_ucsc | Function to convert bigBed to bed file |
| bin_chromosomes | Split chromosomes into bins |
| bin_genome | Function to bin chromosome data acrooss chromosomes |
| bin_targets_cnvkit | Create binned target and anitarget beds from target BED file |
| build_default_binary_list | Build default binaries config |
| build_default_cache_list | Build default cache list |
| build_default_chr_list | Build chromosome list |
| build_default_clonet_dir_list | Build default references |
| build_default_cn_list | Build default references |
| build_default_config | Build default tool configuration |
| build_default_hatchet_config | Build default references |
| build_default_license_list | Build default license list |
| build_default_myriad_module_list | Build default myriad module list |
| build_default_nf_list | Build default nf-core pipeline list |
| build_default_option_list | Build default binaries config |
| build_default_parameter_list | Build default tool configuration |
| build_default_preprocess_config | Build default config for preprocessing step |
| build_default_python_enviroment_list | Build default python enviroment list |
| build_default_reference_list | Build default references |
| build_default_sample_sheet | Build default sample sheet |
| build_default_sif_list | Build default sif list |
| build_default_steps_list | Build default tool configuration |
| build_default_tool_binary_list | Build default tools binaries config |
| build_default_variable_list | Build default binaries config |
| build_flowcell_id | Build dataframe with matched flowcell_id patterns,... |
| build_instrument_id | Build dataframe with matched instrument_id patterns and... |
| build_job | Build job for SGE executor Job constructor only uses the top... |
| build_job_report | Build a job report data structure |
| build_step | Build default tool configuration |
| call_aasuite | Wrapper around assuite |
| call_ascat | Analyze a pair of tumour-normal samples using ASCAT |
| call_coverage_cnvkit | Wrapper around autobin function from CNVkit |
| call_germline_snvs_strelka | Strelka wrapper for germline SNV variant calling |
| call_germline_sv_manta | Manta wrapper for structural variant calling |
| call_get_insert_size_samtools | Filter BAM file by size using samtools |
| call_haplotypecaller_gatk | Variant Calling using HaplotypeCaller |
| call_refphase | Process ASCAT data using REFPHASE |
| call_snvs_strelka | Strelka wrapper for SNV variant calling |
| call_somatic_snvs_strelka | Strelka wrapper for somatic SNV variant calling |
| call_somatic_sv_manta | Manta wrapper for structural variant calling |
| call_sv_manta | Strelka wrapper for SNV variant calling |
| call_variants_strelka | Manta and Strelka wrapper for variant calling |
| check_if_compressed | Check if sample is compressed |
| check_job_limit | Check for job limit in Myriad SGE |
| check_missing | Check if value is missing |
| check_pcf_identity | Writes VCF file from a VCF data.structure |
| check_req_cols | Check required columns in sample sheet |
| check_req_types | Check required variable values for a column |
| circdna_circlemap | Extract Circular DNA Candidates using Circlemap tool |
| circ_quant_rna | Quantify circRNA expression using ciriQuant |
| circ_rna | Generate a quality control (QC) report from a fastaqc file |
| clonet_trento | Process a pair of tumour-normal samples using CLONET |
| clonet_view_trento | View CLONET output |
| cnn_score_variants_gatk | Germline Variant Scoring Using CNN |
| complement_bed | Create BED with antitarget regions with padding |
| compress_and_index_bed_htslib | Compress BED using BGZIP from HTSLIB |
| compress_and_index_vcf_htslib | Compress VCF using BGZIP from HTSLIB |
| compress_bed_htslib | Compress BED using BGZIP from HTSLIB |
| compress_vcf_htslib | Compress VCF using BGZIP from HTSLIB |
| concatenate_bams | Concatenate BAM files in directory. |
| concat_file_list | Concat multiple delimited files |
| concat_vcf | Concatenate a list of vcf files |
| correctLog2_ascat | ascat.correctLogR |
| coverage_cnvkit | Wrapper around autobin function from CNVkit |
| cp_data | cp file/directory This function removes/deletes one or... |
| create_antitarget_cnvkit | Wrapper around antitarget function from CNVkit |
| create_genomic_db_gatk | Wrapper around CreateDBImport from GATK package |
| create_pon_cnvkit | Wrapper around target function from CNVkit |
| create_pon_gatk | Wrapper around CreateSomaticPanelOfNormals from GATK package |
| create_target_cnvkit | Wrapper around target function from CNVkit |
| diagram_cnvkit | Wrapper around reference scatter from CNVkit |
| estimate_contamination_gatk | Estimate sample contamination Gatk |
| evaluate_tf | Get across TF This function calculates coverages for TFBS of... |
| extract_body_vcf | Extract VCF body This function VCF body columns in a easy to... |
| extract_csq_info_vcf | Return tabulated INFO column information to single INFO... |
| extract_descriptors_vcf | Extract VCF header descriptors This function extracts VCF... |
| extract_pass_variants_strelka_vcf | Extract PASS variants in VCF file |
| extract_read_header | Extract the a header for a random read from a sequencing file |
| file_cp | cp file/directory This function removes/deletes one or... |
| file_rm | Remove file/directory This function removes/deletes one or... |
| file_scp | scp file/directory This function scp files from local to... |
| filter_bam | Filter BAM to specific regions |
| filter_bam_by_size_samtools | Filter BAM file by size using samtools |
| filter_chr | Filter BED file by chromosome This function sets and/or... |
| filter_tabulated_vcf | Filter tabulated VCF |
| filter_variant_tranches_gatk | Variant Trench Filtering using GATK |
| find_instrument | Find sequencing instrument name from sequecing information |
| fix_cnvkit | Wrapper around reference function from CNVkit |
| for_id | For each variable in sample sheet |
| gather_bam_files_picard | Wrapper around gatk GatherBamFiles function |
| gather_BQSR_reports_gatk | Wrapper around gatk GatherBQSRReports function |
| generate_BQSR_gatk | Wrapper of BaseRecalibrator function from gatk |
| get_bam_reference_chr | Function to collect chromosome data in bam |
| get_base_fasta | Get reference base in FASTA at genomic position |
| get_coverage | Read file with Genomic Positions |
| get_coverage_tfbs | Get coverage at TFBS This function calculates coverages based... |
| get_fai_reference_chr | Function to collect chromosome data in fasta fai |
| get_file_ext | Get the extension of a file |
| get_file_name | Get the filename of input file This function takes the... |
| get_insert_size_samtools | Filter BAM file by size using samtools |
| get_sq_bam | Function to extract SQ (Reference sequence dictionary) |
| get_tf_from_cnvkit | Filter BAM file by size using samtools |
| get_tf_from_sample | Filter BAM file by size using samtools |
| haplotypecaller_gatk | Variant Calling using HaplotypeCaller |
| ichor_capture | IchorCNA implementation for Capture Panel Data |
| ichorCNA | Generate report for ULP-WGS samples |
| ichor_wgs | Generate a ichorCNA for WGSd |
| index_bam_samtools | Index a BAM file |
| index_bed_htslib | Index BED using TABIX from HTSLIB |
| index_ref_bwa | Index reference genome |
| index_vcf_htslib | Index VCF using TABIX from HTSLIB |
| infer_sequencing_info | Infer sequencing information from sequencing file |
| insertsize_metrics_bam_picard | Generate BAM Insert Size Metrics |
| install_required_tools | Installs all the required tools for the analysis. |
| intersect_file_name | Get sample name from two sample replicates |
| job_validator | Validate job submited in batch on sungrid based cluster |
| learn_orientation_gatk | Create Read Orientation Model for Mutect2 Filter |
| liftOver_ucsc | Function to liftOver files between versions |
| ln_data | cp file/directory This function removes/deletes one or... |
| make_unique_id | Create an unique ID |
| mapq_metrics_bam_samtools | Generate BAM MapQ metrics |
| markdups_gatk | Wrapper for MarkDuplicatesSpark from gatk |
| markdups_picard | Mark duplicated reads |
| mclapply_os | Mclapply implementation for Windows/Linux |
| merge_bams_samtools | Merge BAM files in directory |
| merge_mutect_stats_gatk | Multiregion parallelization across Mutect2 Gatk Variant... |
| metrics_alignqc | Generate quality control metrics for aligned sequences |
| mpileup_samtools | Generate mpileup file from BAM file |
| multisample_clonet_trento | Process multiple tumour samples using CLONET |
| multisample_mutect2_gatk | Multiregion parallelization across Mutect2 Gatk Variant... |
| mutect2_gatk | Variant Calling using Mutect2 |
| mutect_filter_gatk | Filter Mutect2 Calls wrapper for R |
| myriad_module | Load/Unload modules in myriad |
| nest_vcf_body | Nest VCF body |
| new_clonet_trento | Process a pair of tumour-normal samples using CLONET |
| new_flag_stats_samtools | Generate BAM file flagstats |
| new_get_insert_size_samtools | Filter BAM file by size using samtools |
| new_haplotypecaller_gatk | Variant Calling using HaplotypeCaller |
| new_index_bam_samtools | Index a BAM file |
| new_index_stats_samtools | Generate BAM file indexstats |
| new_insertsize_metrics_bam_picard | Generate BAM Insert Size Metrics |
| new_sort_and_index_bam_samtools | Sort and index a sequence file |
| new_sort_bam_samtools | Sort a BAM file |
| new_stats_bam_samtools | Generate BAM file flag and index stats |
| new_tg_summary_metrics_bam_picard | Generate BAM Summary for Targeted data |
| pad_bed | Pad a BED file |
| panel_of_normals_ichorCNA | Generate panel of normals for ichorCNA |
| parallel_apply_BQSR_gatk | Multiregion parallelization of apply_BQSR function |
| parallel_estimate_contamination_gatk | Estimate multis-sample contamination GATK |
| parallel_generate_BQSR_gatk | Multiregion parallelization of generate_BQSR function |
| parallel_pileup_summary_gatk | Generate pileup summary for BAM files |
| parallel_region_filter_bam_by_size_samtools | Filter BAM file by size using samtools in parallel |
| parallel_region_get_insert_size_samtools | Filter BAM file by size using samtools in parallel |
| parallel_regions_mutect2_gatk | Multiregion parallelization across Mutect2 Gatk Variant... |
| parallel_sample_bigBedToBed_ucsc | Parallel implementation of bigBedToBed function |
| parallel_sample_ichor_capture | IchorCNA implementation for Capture Panel Data |
| parallel_samples_call_ascat | Analyze in parallel multiple pair of tumour-normal samples... |
| parallel_samples_mutect2_gatk | Multiregion parallelization across Mutect2 Gatk Variant... |
| parameter_config_check | Check parameter configuration in sample sheet |
| parse_args | Parse tool arguments |
| parse_picard_metrics | Parse HS metrics and WGS metrics picard info |
| parse_read_header | Parse read header |
| parse_summary_picard | Extract Histogram and Metric Information from Picard Summary... |
| parse_tool_parameters | Parse all tool parameters from sample sheet |
| phase_chr_shapeit | Strelka wrapper for SNV variant calling |
| phase_shapeit | Strelka wrapper for SNV variant calling |
| pileup_summary_gatk | Generate a pileup summary for BAM file |
| pipe | Pipe operator |
| ploidy_from_cnr | Wrapper around assuite |
| ploidy_from_cns | Wrapper around assuite |
| plot_cnvkit | Plot CNR across bins |
| plot_coverage_panel | Generate coverage plots for panel on and/or off target... |
| plot_cumulative_cov | Generate cumulative coverage plots for panel on and/or off... |
| prepare_ascat | Prepare ASCAT data from PCF select BAM files |
| preprocess_seq | Preprocess sequencing data |
| preprocess_seq_trento | Generate a quality control (QC) report from a fastaqc file |
| process_ascat | Prepare ASCAT data from PCF select BAM files |
| process_cnvkit | This function functions calls Mutect2 for variant calling. If... |
| process_refphase | Process ASCAT data using REFPHASE |
| process_sample | For each variable in sample sheet |
| qc_fastqc | Generate a quality control (QC) report from a fastaqc file |
| qdel | Wrapper around qdel call for SGE |
| qstat | Wrapper around qstat call for SGE |
| read_and_load_ascat_refphase | Read and load ASCAT style data from rdata files |
| read_bed | Read a BED file This function reads a BED file and stores it... |
| read_bed_circlemap | Read Circle-Map circDNA BED file output |
| read_counter | Generate a WIG file |
| read_counter_region | Generate a WIG file |
| read_extractor_circlemap | Extract Circular Reads using Circlemap tool |
| read_fai | Read reference genome fasta index file |
| read_fasta | Read reference genome fasta file |
| read_gpos | Read file with Genomic Positions |
| read_job_report | Unnest job report |
| read_pileup | Read reference genome fasta file |
| read_vcf | Read a VCF file This function read a VCF file and stores it... |
| realign_circlemap | Extract Circular DNA Candidates using Circlemap Realign tool |
| recal_gatk | Function for base quality recalibration |
| reference_cnvkit | Wrapper around reference function from CNVkit |
| repeat_caller_circlemap | Extract Circular DNA Repeat Candidates using Circlemap tool |
| replace_rg | Wrapper around samtools addreplacerg function |
| rnaseq_summary_metrics_bam_picard | Generate BAM Summary for RNAseq data |
| run_hatchet | Preprocess sequencing data |
| run_meddic2 | Preprocess sequencing data |
| sample_bam_samtools | Sort and index a sequence file |
| scatter_cnvkit | Wrapper around reference scatter from CNVkit |
| segment_cnvkit | Wrapper around reference function from CNVkit |
| seq_info_check | Check sequencing information for samples |
| seqlast | Function to generate seq with trailing ner |
| set_dir | Set the current dir This function sets and/or creates the... |
| set_input_id | Set default environment ID |
| set_inputs | Set main enviroment inputs |
| set_name | Set the current name This function sets a new a name for a... |
| sliding_bin_genome | Function to bin chromosome across_sliding windows |
| sort_and_index_bam_samtools | Sort and index a sequence file |
| sort_bam_samtools | Sort a BAM file |
| sort_vcf | Concatenate a list of vcf files |
| stats_bam_samtools | Generate BAM file flag and index stats |
| stats_flag_samtools | Generate BAM file flagstats |
| stats_index_samtools | Generate BAM file indexstats |
| summary_metrics_bam_picard | Generate BAM General Summary Metrics |
| tabulate_info_vcf | Tabulate INFO column information extracted from VCF file |
| tabulate_vcf | Generate tabulated table from annotate VCF |
| tg_summary_metrics_bam_picard | Generate BAM Summary for Targeted data |
| thisFile | Get current script path |
| trimming_skewer | Adapter sequence trimmer using skewer |
| uncompress_bed_htslib | Uncompress BED using BGZIP from HTSLIB |
| uncompress_vcf_htslib | Uncompress VCF using BGZIP from HTSLIB |
| unnest_vcf_body | Unnest VCF body |
| untabulate_info_vcf | Return tabulated INFO column information to single INFO... |
| validate_arg | Validate tool argument for step |
| validate_input_args | Validate tool args inputs |
| validate_sample_sheet | Validate sample sheet input columns |
| variants_by_filters_vcf | Removes variants with from VCF file vased on the values in... |
| variants_by_type_vcf | Removes variants with from VCF file vased on the values in... |
| wgs_summary_metrics_bam_picard | Generate BAM Summary for WGS data |
| with_env | Set an enviroment for a function |
| write_vcf | Writes VCF file from a VCF data.structure |
