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175 SNPs being called at reference "N" sites in TASSEL 4, reported reference allele is "A". v1.0_(example) open 2014-05-23 2014-05-23 3  
174 MergeIdenticalTaxaPlugin in TASSEL 4.0 v1.0_(example) open 2014-03-19 2014-10-01 5  
169 TASSEL 4 VCF Manipulation v1.0_(example) open Qi Sun 2013-07-17 2013-07-25 5  
162 TASSEL discards hapmap file metadata v1.0_(example) open Terry Casstevens 2013-05-28 2013-06-11 5  
160 ExtractHapmapSubsetPlugin does not exit when no taxa match hapmap. open Peter Bradbury 2013-01-22 2013-01-23 5  
159 UNEAK Pipeline:ArrayIndexOutOfBoundsException open Fei Lu 2013-01-10 2013-01-11 4  
158 ArrayIndexOutOfBoundsException while running UNEAK pipeline None open Fei Lu 2012-12-18 2012-12-18 5  
157 Importing with <Use> and <Format> None open Terry Casstevens 2012-12-07 2013-01-03 5  
154 TagCountToFastqPlugin vs. MergeMultipleTagCountPlugin differ None open Jeff Glaubitz 2012-08-31 2013-01-03 5  
151 genetic distance calculated wrong for hapmap data None open Peter Bradbury 2012-08-16 2012-08-16 5  
150 Manhattan plot miscolored/misplaced SNPs None open Jon Zhang 2012-06-12 2012-06-25 5  
148 Overall genosummary hets None open Terry Casstevens 2012-05-11 2012-06-25 5  
147 Tutorial fails in TASSEL 4 None open Terry Casstevens 2012-04-30 2012-06-25 5  
146 SBitNucleotide.isIndel() None open Ed Buckler 2012-04-10 2013-01-03 5  
142 Chr and position filter does not work together None open Terry Casstevens 2011-11-28 2011-12-07 5  
141 Output LD sliding window None open Terry Casstevens 2011-10-31 2011-11-09 5  
140 MergeMultipleTagCountPlugin java.io.EOFException None open Terry Casstevens 2011-10-15 2012-08-29 5  
139 GBS pipeline - FastqToTBTPlugin None open Terry Casstevens 2011-09-29 2012-08-29 5  
138 GBS pipeline - FastqToTagCountPlugin None open Terry Casstevens 2011-09-29 2012-08-29 5  
135 Number of Permutations (LD) None open Ed Buckler 2011-09-14 2013-01-03 5  
132 Synonimizer not working correctly None open Terry Casstevens 2011-06-27 2011-06-29 5  
131 Load plink format file does not work None open Terry Casstevens 2011-06-03 2011-06-04 5  
127 compression None open Zhiwu Zhang 2011-02-26 2011-04-21 5  
123 GLM: A lot of low P Values None open Peter Bradbury 2011-01-26 2013-01-03 5  
115 Filter sites remove +/- SNPs None open Jon Zhang 2010-11-01 2010-11-02 5  
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