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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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jmaguire 4e0cd6ab84 Now works on single samples and computes metrics. 
Here is an example metrics output from a very tiny region:

	Allele Frequency Metrics (LOD >= 5)
	-------------------------------------------------
	Total loci                         : 14704
	Total called with confidence       : 10920 (74.27%)
	Number of Variants                 : 16 (0.15%) (1/682)
    Fraction of variant sites in dbSNP : 100.00%

Missing:
    Microarray(hapmap) concordance, tp/fp.

Optional:
    Histograms of depth of coverage, LOD, observed allele frequency, etc.



Still to implement:
    Propagate command line argument N (number of chromosomes) into walker to enable pooled calling.
    Take allele frequency priors as input.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@133 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-03-22 15:45:12 +00:00
core/java/src/org/broadinstitute/sting some reformatting and logic cleanup in the comparison functions 2009-03-22 15:36:56 +00:00
doc Describe how GATK finds walkers. Change the example to avoid copying the class file into the walkers directory. 2009-03-19 22:41:12 +00:00
playground Now works on single samples and computes metrics. 2009-03-22 15:45:12 +00:00
settings Update picard to work with new samtools. 2009-03-20 21:51:26 +00:00
testdata Skeleton of new directory structure. 2009-03-11 20:05:05 +00:00
build.xml Added FourBaseCaller as a jar build target. 2009-03-21 17:59:13 +00:00
ivy.xml Update picard to work with new samtools. 2009-03-20 21:51:26 +00:00