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 Calling very rare variants, 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 2nd Jun 2025 at 11:03 by GTN Bot

Added/updated 4 files


Open master 5e95d71
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Created: 2nd Jun 2025 at 11:03

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