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
..
iterators	Move the basic gatk framework into the core subtree.	2009-03-18 23:39:00 +00:00
walkers	Now works on single samples and computes metrics.	2009-03-22 15:45:12 +00:00
PrepareROD.java	Update picard to work with new samtools.	2009-03-20 21:51:26 +00:00