Workflow Type: Galaxy

Calling variants in diploid systems

Associated Tutorial

This workflows is part of the tutorial Calling variants in diploid systems, available in the GTN

Features

Thanks to...

Workflow Author(s): Anton Nekrutenko, Nicola Soranzo

Tutorial Author(s): Anton Nekrutenko, Nicola Soranzo, Khaled Jum'ah

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
GIAB-Ashkenazim-Trio-hg19.bam #main/GIAB-Ashkenazim-Trio-hg19.bam Bam file
  • File
GIAB-Ashkenazim-Trio.tabular #main/GIAB-Ashkenazim-Trio.tabular n/a
  • File

Steps

ID Name Description
2 FreeBayes toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.9+galaxy0
3 VcfAllelicPrimitives: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0
4 SnpEff eff: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0
5 GEMINI load toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2
6 GEMINI_query2 toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy2
7 GEMINI_db_info toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.20.1
8 GEMINI_query1 toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy2

Version History

4.0 (earliest) Created 2nd Jun 2025 at 11:02 by GTN Bot

Added/updated 4 files


Open master 281a8f0
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Views: 45   Downloads: 3   Runs: 0

Created: 2nd Jun 2025 at 11:02

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Total size: 74.1 KB
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