Variant calling from matched tumor/normal sample pair (hg38 version) Version 1
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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 |
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| Estimated tumor tissue purity | #main/Estimated tumor tissue purity | n/a |
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| ID of matched normal sample | #main/ID of matched normal sample | n/a |
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| NORMAL sample forward reads | #main/NORMAL sample forward reads | n/a |
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| NORMAL sample reverse reads | #main/NORMAL sample reverse reads | n/a |
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| Patient sex | #main/Patient sex | n/a |
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| Regions of interest | #main/Regions of interest | n/a |
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| Sample ID (tumor tissue) | #main/Sample ID (tumor tissue) | n/a |
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| TUMOR sample forward reads | #main/TUMOR sample forward reads | n/a |
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| 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 |
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| analysis_metadata | #main/analysis_metadata | n/a |
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| bamqc_html_normal | #main/bamqc_html_normal | n/a |
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| bamqc_html_tumor | #main/bamqc_html_tumor | n/a |
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| bamqc_normal_genome_results | #main/bamqc_normal_genome_results | n/a |
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| bamqc_tumor_genome_results | #main/bamqc_tumor_genome_results | n/a |
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| fastqc_html_normal_fw_after | #main/fastqc_html_normal_fw_after | n/a |
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| fastqc_html_normal_fw_before | #main/fastqc_html_normal_fw_before | n/a |
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| fastqc_html_normal_rv_after | #main/fastqc_html_normal_rv_after | n/a |
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| fastqc_html_normal_rv_before | #main/fastqc_html_normal_rv_before | n/a |
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| fastqc_html_tumor_fw_after | #main/fastqc_html_tumor_fw_after | n/a |
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| fastqc_html_tumor_fw_before | #main/fastqc_html_tumor_fw_before | n/a |
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| fastqc_html_tumor_rv_after | #main/fastqc_html_tumor_rv_after | n/a |
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| fastqc_html_tumor_rv_before | #main/fastqc_html_tumor_rv_before | n/a |
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| multiqc_html_post_trim | #main/multiqc_html_post_trim | n/a |
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| multiqc_html_pre_trim | #main/multiqc_html_pre_trim | n/a |
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Version History
Version 1 (earliest) Created 27th Oct 2023 at 14:48 by Wolfgang Maier
Initial commit
Frozen
Version-1508f246
Creators and SubmitterViews: 3084 Downloads: 198 Runs: 0
Created: 27th Oct 2023 at 14:48
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