Du Novo GTN Tutorial - Variant Calling
3.0

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

Thanks to...

Tutorial Author(s): Anton Nekrutenko, Nick Stoler

gtn star logo followed by the word workflows

Inputs

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

Steps

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

Outputs

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

Version History

3.0 (earliest) Created 25th Jun 2024 at 10:56 by Helena Rasche

Added/updated 4 files


Open master 1efd0ab
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Views: 263   Downloads: 70

Created: 25th Jun 2024 at 10:56

Last updated: 25th Jun 2024 at 10:56

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