Difference between revisions of "FreeBayes"
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Moskalenko (talk | contribs) m (Text replace - "<!--Location--> {{App_Location|app={{#var:app}}|{{#var:ver}}}}" to "") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
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|{{#vardefine:app|freebayes}} | |{{#vardefine:app|freebayes}} | ||
|{{#vardefine:url|http://bioinformatics.bc.edu/marthlab/FreeBayes}} | |{{#vardefine:url|http://bioinformatics.bc.edu/marthlab/FreeBayes}} | ||
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|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
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{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
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FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners. | FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners. | ||
In addition to substantial performance improvements over its predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heterogeneous copy number. FreeBayes is currently under active development. | In addition to substantial performance improvements over its predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heterogeneous copy number. FreeBayes is currently under active development. | ||
| − | + | <!--Modules--> | |
| − | + | ==Environment Modules== | |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | <!-- --> | + | ==System Variables== |
| − | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | |
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* HPC_FREEBAYES_BIN - executable directory | * HPC_FREEBAYES_BIN - executable directory | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
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{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
Latest revision as of 18:55, 12 August 2022
Description
freebayes website
FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners.
In addition to substantial performance improvements over its predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heterogeneous copy number. FreeBayes is currently under active development.
Environment Modules
Run module spider freebayes to find out what environment modules are available for this application.
System Variables
- HPC_FREEBAYES_DIR - installation directory
- HPC_FREEBAYES_BIN - executable directory