Trio Analysis Tutorial

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Workflow Type: Galaxy

Trio Analysis using Synthetic Datasets from RD-Connect GPAP

Associated Tutorial

This workflows is part of the tutorial Trio Analysis Tutorial, available in the GTN

Features

Thanks to...

Tutorial Author(s): Jasper Ouwerkerk, Wolfgang Maier, Helena Rasche, Saskia Hiltemann

Workflow Author(s): Jasper Ouwerkerk

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1096?version=1

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

5.0 (latest) Created 16th Jul 2024 at 14:09 by Helena Rasche

Added/updated 4 files


Open master 92bd1c0

22.0 (earliest) Created 25th Jun 2024 at 10:57 by Helena Rasche

Added/updated 4 files


Frozen 22.0 9ec8ec7
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
EGA
BCFtools
GEMINI
License
MIT License
Activity

Views: 449   Downloads: 163

Created: 25th Jun 2024 at 10:57

Last updated: 25th Jun 2024 at 10:57

help Attributions

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Total size: 235 KB
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