jmaguire 6e180ed44e Unified caller is go. ... AlleleFrequencyWalker and related classes work equally well for 2 or 200 chromosomes. Single Sample Calling: Allele Frequency Metrics (LOD >= 5) ------------------------------------------------- Total loci : 171575 Total called with confidence : 168615 (98.27%) Number of variants : 111 (0.07%) (1/1519) Fraction of variant sites in dbSNP : 87.39% ------------------------------------------------- Hapmap metrics are coming up all zero. Will fix. Pooled Calling: AAF r-squared after EM is 0.99. AAF r-squared after EM for alleles < 20% (in pools of ~100-200 chromosomes) is 0.95 (0.75 before EM) Still not using fractional genotype counts in EM. That should improve r-squared for low frequency alleles. Chores still outstanding: - make a real pooled caller walker (as opposed to my experiment framework). - add fractional genotype counts to EM cycle. - add pool metrics to the metrics class? *shrug* we don't really have truth outside of a contrived experiment... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@380 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-13 12:29:51 +00:00
..
src/org/broadinstitute/sting	Unified caller is go.	2009-04-13 12:29:51 +00:00
test/org/broadinstitute/sting	Added basic performance testing so I can make sure concurrent access doesn't slow down overall fasta access.	2009-04-12 18:05:56 +00:00