Identification of somatic and germline variants from tumor and normal sample pairs tutorial
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Identification of somatic and germline variants from tumor and normal sample pairs tutorial

Associated Tutorial

This workflows is part of the tutorial Identification of somatic and germline variants from tumor and normal sample pairs tutorial, available in the GTN

Features

Thanks to...

Tutorial Author(s): Wolfgang Maier

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1081?version=1

Inputs

ID Name Description Type
01-Feb-2019-CIVic.bed 01-Feb-2019-CIVic.bed n/a
  • File
01-Feb-2019-GeneSummaries.tsv 01-Feb-2019-GeneSummaries.tsv n/a
  • File
SLGFSK-N_231335_r1_chr5_12_17.fastq SLGFSK-N_231335_r1_chr5_12_17.fastq n/a
  • File
SLGFSK-N_231335_r2_chr5_12_17.fastq SLGFSK-N_231335_r2_chr5_12_17.fastq n/a
  • File
SLGFSK-T_231336_r1_chr5_12_17.fastq SLGFSK-T_231336_r1_chr5_12_17.fastq n/a
  • File
SLGFSK-T_231336_r2_chr5_12_17.fastq SLGFSK-T_231336_r2_chr5_12_17.fastq n/a
  • File
Uniprot_Cancer_Genes.13Feb2019.txt Uniprot_Cancer_Genes.13Feb2019.txt n/a
  • File
cgi_genes.txt cgi_genes.txt n/a
  • File
cgi_variant_positions.bed cgi_variant_positions.bed n/a
  • File
dbsnp.b147.chr5_12_17.vcf.gz dbsnp.b147.chr5_12_17.vcf.gz n/a
  • File
hg19.chr5_12_17.fa hg19.chr5_12_17.fa n/a
  • File
hotspots.bed hotspots.bed n/a
  • File

Steps

ID Name Description
12 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
13 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
14 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5
15 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
16 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
17 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5
18 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
19 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
20 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
21 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0
22 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
23 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
24 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
25 Filter toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1
26 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0
27 Filter toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1
28 RmDup toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1
29 RmDup toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1
30 BamLeftAlign toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1
31 BamLeftAlign toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1
32 CalMD toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2
33 CalMD toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2
34 Filter toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1
35 Filter toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1
36 VarScan somatic toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.6
37 SnpEff eff: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1
38 GEMINI load toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2
39 GEMINI annotate toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2
40 GEMINI annotate toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2
41 GEMINI annotate toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2
42 GEMINI annotate toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2
43 GEMINI annotate toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2
44 GEMINI query toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy1
45 GEMINI query toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy1
46 GEMINI query toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy1
47 GEMINI query toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy1
48 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1
49 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1
50 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1
51 Column arrange toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2

Outputs

ID Name Description Type
gene_report_output gene_report_output n/a
  • File

Version History

1.0 (earliest) Created 25th Jun 2024 at 10:55 by Helena Rasche

Added/updated 4 files


Open master 4b434f0
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
FastQC
Trimmomatic
BWA
MultiQC
BamTools
SAMtools
FreeBayes
VarScan
GEMINI
License
Creative Commons Attribution 4.0 International
Activity

Views: 134   Downloads: 47

Created: 25th Jun 2024 at 10:55

Last updated: 25th Jun 2024 at 10:55

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Total size: 330 KB
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