Workflow Type: Galaxy
Calling variants in non-diploid systems
Associated Tutorial
This workflows is part of the tutorial Calling variants in non-diploid systems, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Anton Nekrutenko, Alex Ostrovsky
Tutorial Author(s): Anton Nekrutenko, Alex Ostrovsky
Steps
ID | Name | Description |
---|---|---|
4 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 |
5 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 |
6 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19 |
7 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 |
8 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 |
9 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19 |
10 | MergeSamFiles | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0 |
11 | MarkDuplicates | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0 |
12 | BamLeftAlign | toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.9 |
13 | Filter BAM | toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2 |
14 | FreeBayes | toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.9+galaxy0 |
15 | VCFfilter: | toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3 |
16 | VCFtoTab-delimited: | toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0 |
17 | Cut | Cut1 |
Version History

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Views: 49 Downloads: 3 Runs: 0
Created: 2nd Jun 2025 at 11:03


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