Tassel4 Conversion
Tassel4 Conversion (USER MANUAL UNDER DEVELOPMENT)
Community rating: ?????
This application harnesses the conversion capabilities of the Tassel 3 pipeline in order to facilitate conversion of common GWAS file formats.
Quick Start
- Select the expandable menu that matches your input file format.
- Upload all required input files within that menu.
- Select the Output expandable menu (it will be the last expandable menu option).
- Select the file-format that matches the format you would like to export to from the drop-down list.
- Launch analysis. Once the conversion is completed the converted file will be found within the relevant analysis subfolder with the same name as your input file but with the converted format extension.
- Resources: http://www.maizegenetics.net/tassel/docs/TasselPipelineCLI.pdf
Test Data
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Tassel3 Conversion.
Available Input Formats
Format |
Extension(s) |
|---|---|
HapMap |
.hmp.txt |
Flapjack |
.map, .geno |
FASTA |
.fas |
Genetic Map |
.map, .txt |
HDF5 |
.hdf5 |
VCF |
.vcf |
Available Export Formats
Format |
Extension(s) |
|---|---|
HapMap |
.hmp.txt |
HapMap Diploid |
.hmp.txt |
HDF5 |
..hdf5 |
VCF |
.vcf |
Flapjack |
.map, .geno |
Phylip (Sequential) |
.phy or .ph |
Phylip (Interleaved) |
.phy or .ph |
Tab Delimited Text |
.txt |