Eric Banks d20a25d681 A much better way of choosing the alternate allele(s) to genotype in the SNP model of UG: instead of looking at the sum of base qualities (which can and did lead to us over-genotyping esp. when allowing multiple alternate alleles), we look at the likelihoods themselves (free since we are already calculating likelihoods for all 10 genotypes). Now, even if the base quals exceed some arbitrary threshold, we only bother genotyping an alternate allele when there's a sample for which it is more likely than ref/ref (I can generate weird edge cases where this falls apart, but none that model truly variable sites that we actually want to call). This leads to a huge efficiency improvement esp. for exomes (and esp. for many samples) where we almost always were trying to genotype all 3 alternate alleles. Integration tests change only because ref calls have slight QUAL differences (because the best alt allele is still chosen arbitrarily, but differently).		2011-12-27 16:50:38 -05:00
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R	Protect ourselves when iteration is present but there's only a single iteration in queueJobReport.R	2011-12-19 10:08:38 -05:00
c	…
chainFiles	…
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java	A much better way of choosing the alternate allele(s) to genotype in the SNP model of UG: instead of looking at the sum of base qualities (which can and did lead to us over-genotyping esp. when allowing multiple alternate alleles), we look at the likelihoods themselves (free since we are already calculating likelihoods for all 10 genotypes). Now, even if the base quals exceed some arbitrary threshold, we only bother genotyping an alternate allele when there's a sample for which it is more likely than ref/ref (I can generate weird edge cases where this falls apart, but none that model truly variable sites that we actually want to call). This leads to a huge efficiency improvement esp. for exomes (and esp. for many samples) where we almost always were trying to genotype all 3 alternate alleles. Integration tests change only because ref calls have slight QUAL differences (because the best alt allele is still chosen arbitrarily, but differently).	2011-12-27 16:50:38 -05:00
packages	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Updating the MD5s	2011-12-21 15:14:05 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00