# HG changeset patch
# User Richard Burhans <burhans@bx.psu.edu>
# Date 1374857473 14400
# Node ID 4188853b940b2ba149689e09bb330833a1dc5326
# Parent  fb944979bf353d3f273604058e843dc7aff47eae
Update to Miller Lab devshed revision eb4e61d024db

diff -r fb944979bf35 -r 4188853b940b dpmix.xml
--- a/dpmix.xml	Thu Jul 25 12:01:47 2013 -0400
+++ b/dpmix.xml	Fri Jul 26 12:51:13 2013 -0400
@@ -73,7 +73,7 @@
 
     <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" />
 
-    <param name="switch_penalty" type="float" min="0" value="10" label="Genotype switch penalty" help="Note: Depends on the density of SNPs.  For instance, with 50,000 SNPs in a vertebrate genome, 1.0 might be appropriate, with millions of SNPs, a value between 10 and 100 might be reasonable."/>
+    <param name="switch_penalty" type="float" min="0" value="10" label="Genotype switch penalty" help="Note:  The best choice for the Genotype switch penalty depends on the density of SNPs and the age of the admixture events.  With 50,000 SNPs in a vertebrate genome, 10.0 might be appropriate, with millions of SNPs, 100.0 might work better.  We recommend experimenting with various thresholds on minimal spacing between SNVs (to increase independence), minimal FST between the source populations (to identify &quot;ancestry informative markers&quot;), and Genotype switch penalty, to reach conclusions that are robust to changes in analysis parameters."/>
 
     <conditional name="user_het">
       <param name="choice" type="select" format="integer" label="Heterochromatin info">