Exome Seq Training Pre-Mapped W Cached Ref
5.0

Visit source

Workflow Type: Galaxy

Exome sequencing data analysis for diagnosing a genetic disease; short version starting from pre-mapped reads

Associated Tutorial

This workflows is part of the tutorial Exome Seq Training Pre-Mapped W Cached Ref, available in the GTN

Tutorial Author(s): Wolfgang Maier, Bérénice Batut, Torsten Houwaart, Anika Erxleben, Björn Grüning

Workflow Author(s): Wolfgang Maier

SEEK ID: https://dev.workflowhub.eu/workflows/1108?version=1

ID	Name	Description	Type
Father data	Father data	Pre-mapped reads of the father sample	File
Mother data	Mother data	Pre-mapped reads of the mother sample	File
PEDigree data	PEDigree data	Family tree with sex and phenotype information in PED format	File
Proband data	Proband data	Pre-mapped reads of the child/proband sample	File

ID	Name	Description
4	Samtools view	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0
5	Samtools view	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0
6	Samtools view	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0
7	RmDup	toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1
8	RmDup	toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1
9	RmDup	toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1
10	FreeBayes	toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0
11	bcftools norm	toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy3
12	SnpEff eff:	toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2
13	GEMINI load	toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2
14	GEMINI inheritance pattern	toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1

ID	Name	Description	Type
snpeff_variant_stats	snpeff_variant_stats	n/a	File
normalized_snpeff_annotated_variants	normalized_snpeff_annotated_variants	n/a	File
candidate_mutations	candidate_mutations	n/a	File