Variant calling from matched tumor/normal sample pair (hg38 version) Version 1
Download RO-Crate
Run on GalaxyCall somatic, germline and LoH event variants from PE Illumina sequencing data obtained from matched pairs of tumor and normal tissue samples.
This workflow can be used with whole-genome and whole-exome sequencing data as input. For WES data, parts of the analysis can be restricted to the exome capture kits target regions by providing the optional "Regions of Interest" bed dataset.
The current version uses bwa-mem for read mapping and varscan somatic for variant calling and somatic status classification.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Estimated normal tissue purity | #main/Estimated normal tissue purity | n/a |
|
| Estimated tumor tissue purity | #main/Estimated tumor tissue purity | n/a |
|
| ID of matched normal sample | #main/ID of matched normal sample | n/a |
|
| NORMAL sample forward reads | #main/NORMAL sample forward reads | n/a |
|
| NORMAL sample reverse reads | #main/NORMAL sample reverse reads | n/a |
|
| Patient sex | #main/Patient sex | n/a |
|
| Regions of interest | #main/Regions of interest | n/a |
|
| Sample ID (tumor tissue) | #main/Sample ID (tumor tissue) | n/a |
|
| TUMOR sample forward reads | #main/TUMOR sample forward reads | n/a |
|
| TUMOR sample reverse reads | #main/TUMOR sample reverse reads | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Set hard-coded internal name for normal sample | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 8 | Set hard-coded internal name for tumor sample | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 12 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 13 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 14 | Trimmomatic | toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 |
| 15 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 16 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 17 | Trimmomatic | toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 |
| 18 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0 |
| 19 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 20 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
| 21 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 22 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 23 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9 |
| 24 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
| 25 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 26 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 27 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0 |
| 28 | Samtools view -H | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 |
| 29 | Build list | __BUILD_LIST__ |
| 30 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9 |
| 31 | Analysis run metadata | Convert characters1 |
| 32 | Select | Grep1 |
| 33 | Relabel identifiers | __RELABEL_FROM_FILE__ |
| 34 | Extract canonical chromosomes as BED | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 |
| 35 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 |
| 36 | Effective regions of interest | pick_value |
| 37 | RmDup | toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 |
| 38 | BamLeftAlign | toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1 |
| 39 | CalMD | toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2 |
| 40 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 |
| 41 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 |
| 42 | Normal Reads | __EXTRACT_DATASET__ |
| 43 | Tumor reads | __EXTRACT_DATASET__ |
| 44 | QualiMap BamQC | toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3 |
| 45 | QualiMap BamQC | toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3 |
| 46 | VarScan somatic | toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.6 |
| 47 | Extract dataset | __EXTRACT_DATASET__ |
| 48 | Extract dataset | __EXTRACT_DATASET__ |
| 49 | Split file | toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 |
| 50 | Split file | toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 |
| 51 | Apply rules | __APPLY_RULES__ |
| 52 | Apply rules | __APPLY_RULES__ |
| 53 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
| 54 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
| 55 | Select | Grep1 |
| 56 | Select | Grep1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| VarScan Output | #main/VarScan Output | n/a |
|
| analysis_metadata | #main/analysis_metadata | n/a |
|
| bamqc_html_normal | #main/bamqc_html_normal | n/a |
|
| bamqc_html_tumor | #main/bamqc_html_tumor | n/a |
|
| bamqc_normal_genome_results | #main/bamqc_normal_genome_results | n/a |
|
| bamqc_tumor_genome_results | #main/bamqc_tumor_genome_results | n/a |
|
| fastqc_html_normal_fw_after | #main/fastqc_html_normal_fw_after | n/a |
|
| fastqc_html_normal_fw_before | #main/fastqc_html_normal_fw_before | n/a |
|
| fastqc_html_normal_rv_after | #main/fastqc_html_normal_rv_after | n/a |
|
| fastqc_html_normal_rv_before | #main/fastqc_html_normal_rv_before | n/a |
|
| fastqc_html_tumor_fw_after | #main/fastqc_html_tumor_fw_after | n/a |
|
| fastqc_html_tumor_fw_before | #main/fastqc_html_tumor_fw_before | n/a |
|
| fastqc_html_tumor_rv_after | #main/fastqc_html_tumor_rv_after | n/a |
|
| fastqc_html_tumor_rv_before | #main/fastqc_html_tumor_rv_before | n/a |
|
| multiqc_html_post_trim | #main/multiqc_html_post_trim | n/a |
|
| multiqc_html_pre_trim | #main/multiqc_html_pre_trim | n/a |
|
Version History
Version 1 (earliest) Created 27th Oct 2023 at 14:48 by Wolfgang Maier
Initial commit
Frozen
Version-1508f246
Creators and SubmitterViews: 3230 Downloads: 207 Runs: 0
Created: 27th Oct 2023 at 14:48
Tags AttributionsNone
Related items
Teams: usegalaxy-eu, GalaxyProject SARS-CoV-2
Organizations: European Galaxy Team
https://orcid.org/0000-0002-9464-6640
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, MOLGENIS, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC, Probabilistic graphical models, GenX, Snakemake-Workflows, ODA, IPK BIT, CO2MICS Lab, FAME, CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus, Quadram Institute Bioscience - Bioinformatics, HecatombDevelopment, Institute of Human Genetics, Testing RO Crates, Test Team, Applied Computational Biology at IEG/HMGU, INFRAFRONTIER workflows, OME, TransBioNet, OpenEBench, Bioinformatics and Biostatistics (BIO2 ) Core, VIB Bioinformatics Core, CRC Cohort, ICAN, MustafaVoh, Single Cell Unit, CO-Graph, emo-bon, TestEMBL-EBIOntology, CINECA, Toxicology community, Pitagora-Network, Workflows Australia, Medizinisches Proteom-Center, Medical Bioinformatics, AGRF BIO, EU-Openscreen, X-omics, ELIXIR Belgium, URGI, Size Inc, GA-VirReport Team, The Boucher Lab, Air Quality Prediction, pyiron, CAPSID, Edinburgh Genomics, Defragmentation TS, NBIS, Phytoplankton Analysis, Seq4AMR, Workflow registry test, Read2Map, SKM3, ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression, de.NBI Cloud, Meta-NanoSim, ILVO Plant Health, EMERGEN-BIOINFO, KircherLab, Apis-wings, BCCM_ULC, Dessimoz Lab, TRON gGmbH, GEMS at MLZ, Computational Science at HZDR, Big data in biomedicine, TRE-FX, MISTIC, Guigó lab, Statistical genetics, Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation, WES, Bioinformatics Unit @ CRG, Bioinformatics Innovation Lab, BSC-CES, ELIXIR Proteomics, Black Ochre Data Labs, Zavolan Lab, Metabolomics-Reproducibility, Team Cardio, NGFF Tools, Bioinformatics workflows for life science, Workflows for geographic science, Pacific-deep-sea-sponges-microbiome, CSFG, SNAKE, Katdetectr, INFRAFRONTIER GmbH, PerMedCoE, Euro-BioImaging, EOSC-Life WP3 OC Team, cross RI project, ANSES-Ploufragan, SANBI Pathogen Bioinformatics, Biodata Analysis Group, DeSci Labs, Erasmus MC - Viroscience Bioinformatics, ARA-dev, Mendel Centre for Plant Genomics and Proteomics, Metagenomic tools, WorkflowEng, Polygenic Score Catalog, bpm, scNTImpute, Systems Biotechnology laboratory, Cimorgh IT solutions, MLme: Machine Learning Made Easy, Hurwitz Lab, Dioscuri TDA, Scipion CNB, System Biotechnology laboratory, yPublish - Bioinfo tools, NIH CFDE Playbook Workflow Partnership, MMV-Lab, EMBL-CBA, EBP-Nor, Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data, Bioinformatics Laboratory for Genomics and Biodiversity (LBGB), multi-analysis dFC, CholGen, RNA group, Plant Genomes Pipelines in Galaxy, Pathogen Genomic Laboratory, Chemical Data Lab, JiangLab, Pangenome database project, HP2NET - Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment, Center for Open Bioimage Analysis, Generalized Open-Source Workflows for Atomistic Molecular Dynamics Simulations of Viral Helicases, Historical DNA genome skimming, QCDIS, Peter Menzel's Team, NHM Clark group, ESRF Workflow System (Ewoks), Kalbe Bioinformatics, Nextflow4Metabolomics, GBCS, CEMCOF, Jackson Laboratory NGS-Ops, Schwartz Lab, BRAIN - Biomedical Research on Adult Intracranial Neoplasms, Cancer Therapeutics and Drug Safety, Deepdefense, Mid-Ohio Regional Planning Commission, MGSSB, Institute for Human Genetics and Genomic Medicine Aachen, FengTaoSMU, EGA, Plant-Food-Research-Open, KrauthammerLab, Geo Workflows, grassland pDT, FunGIALab, CRIM - Computer Research Institute of Montréal, Medvedeva Lab, Metagenlab, FAIR-EASE, Protein-protein and protein-nucleic acid binding site prediction research, Culhane Lab, IDUN - Drug Delivery and Sensing, Edge Computing DAG Task Scheduling Research Group, Stratum corneum nanotexture feature detection using deep learning and spatial analysis: a non-invasive tool for skin barrier assessment, COPO, Taudière group, ErasmusMC Clinical Bioinformatics, interTwin, fluid flow modeling, EnrichDO, WorkflowResearch, Application Security - Test Crypt4GH solutions
Web page: Not specified
Space: Independent Teams
Public web page: https://usegalaxy.eu
