Quals coming soon (four-base)
QHAT : Most likely alt allele freq (unconstrained by number of chromosomes).
QSTAR : Most likely alt allele freq (constrained by number of chromosomes).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@402 348d0f76-0448-11de-a6fe-93d51630548a
EVEN MORE verbosity to come!
Tremble in anticipation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@382 348d0f76-0448-11de-a6fe-93d51630548a
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
- AlleleMetrics and AlleleMetricrsWalker are now ready to take a list of clasess that implement the AllelicVariant interface
- Switched a genome location in AlleleFrequencyEstimate from String to GenomeLoc which makes way more sense.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@280 348d0f76-0448-11de-a6fe-93d51630548a
- output GFF lines to a file (specified by a command line argument)
- improve the GFF output string
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@240 348d0f76-0448-11de-a6fe-93d51630548a
still need to add printing GFF intervals for stretches of confident reference calls.
does the GFF ROD class handle intervals?? We'll find out. >:)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@225 348d0f76-0448-11de-a6fe-93d51630548a
jmaguire
andrewk
depristo
hanna