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
Inputs
ID | Name | Description | Type |
---|---|---|---|
Trimmed reads (mate 1) | #main/Trimmed reads (mate 1) | n/a |
|
Trimmed reads (mate 2) | #main/Trimmed reads (mate 2) | n/a |
|
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 |
|
_anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
Version History

Creators
Not specifiedSubmitter
Discussion Channel
Activity
Views: 48 Downloads: 4 Runs: 0
Created: 2nd Jun 2025 at 11:03


None