Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC
1.0

Workflow Type: Galaxy

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.

Associated Tutorial

This workflows is part of the tutorial Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC, available in the GTN

Features

Thanks to...

Tutorial Author(s): Khaled Jum'ah, Katarzyna Kamieniecka, Wolfgang Maier, David Salgado, Krzysztof Poterlowicz

Workflow Author(s): khaled Jumah, Katarzyna Kamieniecka, Wolfgang Maier, Krzysztof Poterlowicz, poterlowicz-lab

gtn star logo followed by the word workflows

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_sample_info out_sample_info n/a
  • File
out_sample_coord out_sample_coord n/a
  • File
out_control_raw out_control_raw n/a
  • File
out_sample_raw out_sample_raw n/a
  • File
out_ratio_log2_circos out_ratio_log2_circos n/a
  • File
out_chr_sorted_circos out_chr_sorted_circos n/a
  • File
out_gc_profile out_gc_profile n/a
  • File
out_mg_log2_png out_mg_log2_png n/a
  • File
out_mg_png out_mg_png n/a
  • File
out_sample_subclones out_sample_subclones n/a
  • File
out_sample_ratio out_sample_ratio n/a
  • File
output_png output_png n/a
  • File

Version History

1.0 (earliest) Created 25th Jun 2024 at 10:59 by Helena Rasche

Added/updated 4 files


Open master 24fe8ae
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Views: 297   Downloads: 83

Created: 25th Jun 2024 at 10:59

Last updated: 25th Jun 2024 at 10:59

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