Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC
Version 1

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Workflow Type: Galaxy

Stable

This workflow is created as part of a tutorial listed on GTN. The workflow shows the steps in human copy number variance detection using the Contrl_FREEC tool.

SEEK ID: https://workflowhub.eu/workflows/676?version=1

DOI: 10.48546/workflowhub.workflow.676.1

Inputs

ID	Name	Description	Type
Normal_r1.fastq.gz	Normal_r1.fastq.gz	n/a	File
Normal_r2.fastq.gz	Normal_r2.fastq.gz	n/a	File
Tumor_r1.fastq.gz	Tumor_r1.fastq.gz	n/a	File
Tumor_r2.fastq.gz	Tumor_r2.fastq.gz	n/a	File
capture_targets_chr5_12_17.bed	capture_targets_chr5_12_17.bed	n/a	File

Steps

ID	Name	Description
3	Create text file	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0
6	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
7	Trimmomatic	toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy0
8	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
9	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
10	Trimmomatic	toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy0
11	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
12	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
13	Map with BWA-MEM	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2
14	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
15	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
16	Map with BWA-MEM	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2
17	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
18	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
19	Build list	__BUILD_LIST__
20	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
21	Relabel identifiers	__RELABEL_FROM_FILE__
22	Samtools view	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0
23	RmDup	toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1
24	BamLeftAlign	toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6
25	Samtools calmd	toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.3
26	Samtools view	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0
27	Samtools view	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0
28	Select	Grep1
29	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
30	Samtools view	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0
31	Extract Tumor read	__EXTRACT_DATASET__
32	Extract normal read	__EXTRACT_DATASET__
33	Control-FREEC	toolshed.g2.bx.psu.edu/repos/iuc/control_freec/control_freec/11.6+galaxy2
34	Circos	toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9

Outputs

ID	Name	Description	Type
out_ratio_log2_circos	out_ratio_log2_circos	n/a	File
out_chr_sorted_circos	out_chr_sorted_circos	n/a	File
output_png	output_png	n/a	File

Version History

Version 1 (earliest) Created 23rd Nov 2023 at 17:19 by Khaled Jum'ah

This workflow was made to show the steps required to detect the copy number variants in WES datasets using the Control-FREEC tool

Frozen Version-1 c70bf0b

Creators and Submitter

Creators

khaled Jumah
Katarzyna Kamieniecka
Wolfgang Maier
Krzysztof Poterlowicz

Additional credit

poterlowicz-lab

Submitter

Khaled Jum'ah

Citation

Jumah, K., Kamieniecka, K., Maier, W., & Poterlowicz, K. (2024). Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.676.1

License

GNU General Public License v3.0 only

Activity

Views: 3227 Downloads: 463 Runs: 1

Created: 23rd Nov 2023 at 17:19

Annotated Properties

Topic annotations

Copy number variation, Genetic variation, Data visualisation

Operation annotations

Copy number variation detection, Genetic mapping, Sequencing quality control, Visualisation

Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC Version 1