Du Novo GTN Tutorial - Variant Calling
3.0

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Workflow Type: Galaxy

Run this on the trimmed consensus reads (DCS or SSCS) from Du Novo.

Associated Tutorial

This workflows is part of the tutorial Du Novo GTN Tutorial - Variant Calling, available in the GTN

Tutorial Author(s): Anton Nekrutenko, Nick Stoler

SEEK ID: https://dev.workflowhub.eu/workflows/1089?version=1

ID	Name	Description	Type
Trimmed reads (mate 1)	#main/Trimmed reads (mate 1)	n/a	File
Trimmed reads (mate 2)	#main/Trimmed reads (mate 2)	n/a	File

ID	Name	Description
2	Map with BWA-MEM	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
3	BamLeftAlign	toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.1.0.46-0
4	Naive Variant Caller (NVC)	toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/naive_variant_caller/0.0.4
5	Variant Annotator	toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2
6	Filter	Filter1

ID	Name	Description	Type
_anonymous_output_3	#main/_anonymous_output_3	n/a	File
_anonymous_output_4	#main/_anonymous_output_4	n/a	File

Added/updated 4 files

Open master 1efd0ab

Creators and Submitter

Not specified

Discussion Channel

GTN Matrix

Tools

BWA

License

Activity

Views: 432 Downloads: 104

Created: 25th Jun 2024 at 10:56

Last updated: 25th Jun 2024 at 10:56