6e180ed44e
AlleleFrequencyWalker and related classes work equally well for 2 or 200 chromosomes.
Single Sample Calling:
Allele Frequency Metrics (LOD >= 5)
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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%
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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
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| build.xml | ||
| ivy.xml | ||