comparison freebayes-d291dc763c4c/freebayes.xml @ 1:5022cd74093c draft

Uploaded

0:9a7e8a919c78

      <param name="options_type_selector" value="basic"/>
      <output name="output_vcf" file="freebayes_out_1.vcf.contains" compare="contains"/>
    </test>
  </tests>
  <help>
**What it does**

This tool uses FreeBayes 0.9.9 to call SNPS given a reference sequence and a BAM alignment file.

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. 

Go `here &lt;http://bioinformatics.bc.edu/marthlab/FreeBayes&gt;`_ for details on FreeBayes.

or `here &lt;https://github.com/ekg/freebayes&gt;`_ 
------

**Inputs**

FreeBayes accepts an input aligned BAM file.

                   time and improves scaling performance in large populations.


------

**Citation**

For the underlying tool, please cite `Erik Garrison and Gabor Marth. Haplotype-based variant detection from short-read sequencing <http://arxiv.org/abs/1207.3907>`_.

If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*

  </help>
</tool>

1:5022cd74093c

      <param name="options_type_selector" value="basic"/>
      <output name="output_vcf" file="freebayes_out_1.vcf.contains" compare="contains"/>
    </test>
  </tests>
  <help>
      
**What it does**

This tool uses FreeBayes 0.9.9 to call SNPS given a reference sequence and a BAM alignment file.

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. 

Go FreeBayesMarth_ for details on FreeBayes.

or FreeBayesGit_ for source

------

**Inputs**

FreeBayes accepts an input aligned BAM file.

                   time and improves scaling performance in large populations.


------


**Citation**

For the underlying tool, please cite `Erik Garrison and Gabor Marth. Haplotype-based variant detection from short-read sequencing <http://arxiv.org/abs/1207.3907>`_.

If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*

.. _FreeBayesMarth: http://bioinformatics.bc.edu/marthlab/FreeBayes

.. _FreeBayesGit: https://github.com/ekg/freebayes

.. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html
  </help>
</tool>