depristo
|
6ffcaa0afe
|
Can run R scripts on the command line
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3750 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-07-09 00:13:18 +00:00 |
rpoplin
|
233a652161
|
Making the dotted quartile lines more clear.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2772 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-02-03 22:23:09 +00:00 |
|
rpoplin
|
16da5011c0
|
Added a new option for indicating the mean number of variants on the AnalyzeAnnotations plots. This way one can say, for example, filtering at this point will keep 75 percent of all the variants.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2744 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-01-29 21:58:31 +00:00 |
|
rpoplin
|
c6cc844e55
|
Added -name argument to AnalyzeAnnotations that allows one to specify the name of the annotation to be used on the plots. Instead of seeing AB and DP, one can add -name AB,AlleleBalance -name DP,Depth
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2742 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-01-29 20:48:53 +00:00 |
|
rpoplin
|
4f29a1d4f6
|
AnalyzeAnnotations now plots true positive rate instead of percentage of variants found in the truth set. Committing GCContentCovariate to help people experiment with correcting the pilot3/Kristian base calling error mode in slx.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2740 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-01-29 20:01:56 +00:00 |
|
rpoplin
|
79c4cc1db7
|
AnalyzeAnnotations now breaks out titv by calls in hapmap and also plots true positive rates. Any RODs passed in whose name starts with 'truth' is considered to be the truth set.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2726 348d0f76-0448-11de-a6fe-93d51630548a
|
2010-01-28 21:41:23 +00:00 |