gatk-3.8

History

delangel f64b6fddc1 Major changes/improvements to indel genotyper: a) Redid way to compute path metrics in indel error model. Paper formulation where we have an anchor point in the alignemt between read and haplotype won't work in practice except in nice data sets that are perfectly indel-realigned and that are well mapped by aligner. New formulation doesn't assume this, and it's actually simpler and uses less code. It now resembles more a classic SW dynamic programming formulation but it still preserves the HMM probabilistic formulation. b) Added a programmable call threshold, set by command line. c) Use now sample name from BAM file, remove -sampleName argument. d) Simplify loop to compute read-haplotype likelihoods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4311 348d0f76-0448-11de-a6fe-93d51630548a	2010-09-19 23:47:31 +00:00
..
net/sf/picard/reference	Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.	2010-09-12 15:07:38 +00:00
org/broadinstitute/sting	Major changes/improvements to indel genotyper:	2010-09-19 23:47:31 +00:00

delangel f64b6fddc1 Major changes/improvements to indel genotyper:

a) Redid way to compute path metrics in indel error model. Paper formulation where we have an anchor point in the alignemt between read and haplotype won't work in practice except in nice data sets that are perfectly indel-realigned and that are well mapped by aligner. New formulation doesn't assume this, and it's actually simpler and uses less code. It now resembles more a classic SW dynamic programming formulation but it still preserves the HMM probabilistic formulation. 
b) Added a programmable call threshold, set by command line.
c) Use now sample name from BAM file, remove -sampleName argument.
d) Simplify loop to compute read-haplotype likelihoods.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4311 348d0f76-0448-11de-a6fe-93d51630548a

2010-09-19 23:47:31 +00:00

net/sf/picard/reference

Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.

2010-09-12 15:07:38 +00:00

org/broadinstitute/sting

Major changes/improvements to indel genotyper:

2010-09-19 23:47:31 +00:00