gatk-3.8

History

Mark DePristo 90f59803fd MaxAltAlleles now defaults to 6, no more MaxAltAllelesForIndels -- Updated StandardCallerArgumentCollection to remove MaxAltAllelesForIndels. Previous argument is deprecated with meaningful doc message for people to use maxAltAlleles -- All constructores, factory methods, and test builders and their users updated to provide just a single argument -- Updating MD5s for integration tests that change due to genotyping more alleles -- Adding more alleles to genotyping results in slight changes in the QUAL value for multi-allelic loci where one or more alleles aren't polymorphic. That's simply due to the way that alternative hypotheses contribute as reference evidence against each true allele. The effect can be large (new qual = old qual / 2 in one case here). -- If we want more precision in our estimates we could decide (Eric, should we discuss?) to actually separately do a discovery phase in the genotyping, eliminate all variants not considered polymorphic, and then do a final round of calling to get the exact QUAL value for only those that are segregating. This would have the value of having the QUAL stay constant as more alleles are genotyped, at the cost of some code complexity increase and runtime. Might be worth it through	2012-10-22 13:47:56 -04:00
..
gatk/walkers	MaxAltAlleles now defaults to 6, no more MaxAltAllelesForIndels	2012-10-22 13:47:56 -04:00
utils/pairhmm	Refactoring the PairHMM util class to allow for multiple implementations which can be specified by the callers via an enum argument. Adding an optimized PairHMM implementation which caches per-read calculations as well as a logless implementation which drastically reduces the runtime of the HMM while also increasing the precision of the result. In the HaplotypeCaller we now lexicographically sort the haplotypes to take maximal benefit of the haplotype offset optimization which only recalculates the HMM matrices after the first differing base in the haplotype. Many thanks to Mauricio for all the initial groundwork for these optimizations. The change to the one HC integration test is in the fourth decimal of HaplotypeScore.	2012-10-20 16:38:18 -04:00

Mark DePristo 90f59803fd MaxAltAlleles now defaults to 6, no more MaxAltAllelesForIndels

-- Updated StandardCallerArgumentCollection to remove MaxAltAllelesForIndels. Previous argument is deprecated with meaningful doc message for people to use maxAltAlleles
-- All constructores, factory methods, and test builders and their users updated to provide just a single argument
-- Updating MD5s for integration tests that change due to genotyping more alleles
-- Adding more alleles to genotyping results in slight changes in the QUAL value for multi-allelic loci where one or more alleles aren't polymorphic.  That's simply due to the way that alternative hypotheses contribute as reference evidence against each true allele.  The effect can be large (new qual = old qual / 2 in one case here).
-- If we want more precision in our estimates we could decide (Eric, should we discuss?) to actually separately do a discovery phase in the genotyping, eliminate all variants not considered polymorphic, and then do a final round of calling to get the exact QUAL value for only those that are segregating.  This would have the value of having the QUAL stay constant as more alleles are genotyped, at the cost of some code complexity increase and runtime.  Might be worth it through

2012-10-22 13:47:56 -04:00

gatk/walkers

MaxAltAlleles now defaults to 6, no more MaxAltAllelesForIndels

2012-10-22 13:47:56 -04:00

utils/pairhmm

Refactoring the PairHMM util class to allow for multiple implementations which can be specified by the callers via an enum argument. Adding an optimized PairHMM implementation which caches per-read calculations as well as a logless implementation which drastically reduces the runtime of the HMM while also increasing the precision of the result. In the HaplotypeCaller we now lexicographically sort the haplotypes to take maximal benefit of the haplotype offset optimization which only recalculates the HMM matrices after the first differing base in the haplotype. Many thanks to Mauricio for all the initial groundwork for these optimizations. The change to the one HC integration test is in the fourth decimal of HaplotypeScore.

2012-10-20 16:38:18 -04:00