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changeset 6:73e1e4d0b419 draft default tip

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Deprecated this version
author Lance Parsons <lparsons@princeton.edu>
date Fri, 25 May 2012 13:20:06 -0400
parents c1f3ee7b5003
children
files README freebayes.xml
diffstat 2 files changed, 13 insertions(+), 1 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Fri May 25 13:20:06 2012 -0400
@@ -0,0 +1,12 @@
+This tool was based on an early version of the Freebayes Galaxy wrapper that was included with Galaxy.  Since then, the included tool written by Daniel Blankenberg has been updated and is generally preferred since it works with newer versions of Freebayes and supports more options.
+
+This tool uses Freebayes to call SNPS given a reference sequence and a BAM alignment file.
+http://bioinformatics.bc.edu/marthlab/FreeBayes
+
+Base alignment quality (BAQ) adjustment is a quality smoothing filter which applies a hidden 
+markov model of read genesis to each alignment independently.  This is currently implemented
+by samtools fillmd.  (See Biological Sequence Analysis Probabilistic Models of Proteins and 
+Nucleic Acids by Durbin et. al. for more details.)
+
+
+Updated in 2011 by Lance Parsons <lparsons@princeton.edu>, Lewis-Sigler Institute for Integrative Genomics, Princeton University
--- a/freebayes.xml	Fri May 25 13:09:44 2012 -0400
+++ b/freebayes.xml	Fri May 25 13:20:06 2012 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="freebayes_wrapper_princeton" name="Call SNPS with Freebayes (beta)" version="0.9.0.a">
+<tool id="freebayes_wrapper_princeton" name="Call SNPS with Freebayes (DEPRECATED)" version="0.9.0.a">
   <requirements>
     <requirement type="package" version="0.9.0">freebayes</requirement>
     <requirement type="package">samtools</requirement>