zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk3的最后一个经典版本3.8
1,366 Commits
1 Branch
0 Tags
257 MiB
Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
Go to file
hanna 21d1eba502 Cleaned division of responsibilities between arguments to map function. Reference has been changed 
from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-08-04 21:01:37 +00:00
R Updated python files 2009-07-07 14:15:39 +00:00
c Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
packages Added indel cleaner and quality scores recalibrator to the GATK package. 2009-07-24 16:20:38 +00:00
perl A little gadget to select random samples from input stream(s) of unknown length. By default, selects a single line (with probability 1/TOTAL_NUMBER_OF_LINES_READ), with -N option randomly selects specified number of lines. Can read from STDIN or from arbitrary number of input streams (all streams will be merged). Examples:\n cat file1 file2 file3 | randomSampleFromStream.pl -N 5 \n\n or \n randomSampleFromStream.pl file1 file2 file3 2009-07-31 18:55:14 +00:00
python Script that performs all the processing steps from raw Illumina reads through to analysis of barcoding and hybrid selection efficience as documented in the GATK tutorial; can automatically run all steps in series on the farm. 2009-07-31 00:22:53 +00:00
settings Switched to Reflections (http://code.google.com/p/reflections/) project for 2009-07-21 18:32:22 +00:00
shell Version 0.2.1 (released) of the TableRecalibrator 2009-06-25 22:50:55 +00:00
testdata Derive examples from real data. 2009-07-10 04:21:37 +00:00
build.xml Exclude secondary base caller code from playground jar. Still TODO: figure 2009-07-30 21:02:46 +00:00
ivy.xml Switched to Reflections (http://code.google.com/p/reflections/) project for 2009-07-21 18:32:22 +00:00