Du Novo GTN Tutorial - Variant Calling 3.0
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Run on GalaxyRun 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
master
Creators and Submitter
Views: 234 Downloads: 30 Runs: 0
Created: 2nd Jun 2025 at 11:03
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