Workflow Type: Galaxy
Stable

To discover causal mutations of inherited diseases it’s common practice to do a trio analysis. In a trio analysis DNA is sequenced of both the patient and parents. Using this method, it’s possible to identify multiple inheritance patterns. Some examples of these patterns are autosomal recessive, autosomal dominant, and de-novo variants, which are represented in the figure below. To elaborate, the most left tree shows an autosomal dominant inhertitance pattern where the offspring inherits a faulty copy of the gene from one of the parents.

To discover these mutations either whole exome sequencing (WES) or whole genome sequencing (WGS) can be used. With these technologies it is possible to uncover the DNA of the parents and offspring to find (shared) mutations in the DNA. These mutations can include insertions/deletions (indels), loss of heterozygosity (LOH), single nucleotide variants (SNVs), copy number variations (CNVs), and fusion genes.

In this workflow we will also make use of the HTSGET protocol, which is a program to download our data securely and savely. This protocol has been implemented in the EGA Download Client Tool: toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/4.0.0+galaxy0 tool, so we don’t have to leave Galaxy to retrieve our data.

We will not start our analysis from scratch, since the main goal of this tutorial is to use the HTSGET protocol to download variant information from an online archive and to find the causative variant from those variants. If you want to learn how to do the analysis from scratch, using the raw reads, you can have a look at the Exome sequencing data analysis for diagnosing a genetic disease tutorial.

Inputs

ID Name Description Type
pedigree pedigree n/a
  • File

Steps

ID Name Description
0 EGA Download Client toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0
1 EGA Download Client toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0
3 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
4 EGA Download Client toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0
5 Convert compressed file to uncompressed. CONVERTER_gz_to_uncompressed
6 Column Regex Find And Replace Add chr prefix toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1
7 bcftools norm toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1
8 Filter Filter1
9 bcftools merge toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10
10 SnpEff eff: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1
11 Convert uncompressed file to compressed CONVERTER_uncompressed_to_gz
12 gene.iobio visualisation toolshed.g2.bx.psu.edu/repos/iuc/geneiobio/gene_iobio_display_generation_iframe/4.7.1
13 Case 5 GEMINI Database toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2
14 Case 5 GEMINI Inheritance pattern toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1

Outputs

ID Name Description Type
EGA Download Client: authorized datasets EGA Download Client: authorized datasets n/a
  • File
List of files in EGAD00001008392 List of files in EGAD00001008392 n/a
  • File
List of Case 5 VCFs List of Case 5 VCFs n/a
  • File
Case 5 VCFs.gz Case 5 VCFs.gz n/a
  • File
Case 5 VCFs Case 5 VCFs n/a
  • File
Case 5 VCFs (Fixed Header and Chr) Case 5 VCFs (Fixed Header and Chr) n/a
  • File
Case 5 Normalized VCFs Case 5 Normalized VCFs n/a
  • File
Case 5 Normalized VCFs (Removed ) Case 5 Normalized VCFs (Removed ) n/a
  • File
Case 5 Merged VCF Case 5 Merged VCF n/a
  • File
_anonymous_output_1 _anonymous_output_1 n/a
  • File
Case 5 SnpEff Annotated vcf Case 5 SnpEff Annotated vcf n/a
  • File
SnpEff Annotated vcf_bgzip SnpEff Annotated vcf_bgzip n/a
  • File
Case 5 gene.iobio results Case 5 gene.iobio results n/a
  • File
GEMINI Database GEMINI Database n/a
  • File
Case 5 GEMINI results Case 5 GEMINI results n/a
  • File

Version History

Version 2 (latest) Created 1st Mar 2023 at 15:35 by Helena Rasche

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Frozen Version-2 6e888a8

Version 1 (earliest) Created 9th Jun 2022 at 09:32 by Helena Rasche

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Frozen Version-1 d6327c5
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Citation
Ouwerkerk, J. (2023). Trio Analysis. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.363.2
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Created: 9th Jun 2022 at 09:32

Last updated: 1st Mar 2023 at 15:20

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