gatk3的最后一个经典版本3.8

Guillermo del Angel d5d0e94a11 a) Updating for posterity original scripts for VQSR project consensus (snp and indel) so that they use newest GATK syntax (also they were not run in the end). b) New scripts for redoing indel GL's, jobs are split per sample and per chromosome. ... Another script (PhaseIndelRedoCombining.scala) does the combining of all pieces - not the best solution, but best for development/debugging to have two separate entities. c) Experimental walker to assess GL concordance of two callsets - just accumulates squared error between each sample and site GL's and outputs at the end. d) Another one-off to fill a callset of given GL's with greedy genotypes (genotype that maximizes PL) to have more meaningful metrics and QC of a given GL file.		2011-12-19 16:50:52 +01:00
public	Adding option to VariantAnnotator to do strict allele matching when annotating with comp track concordance.	2011-12-18 15:27:23 -05:00
settings	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	Extensive unit test for GenotypeContextUnitTest	2011-11-20 18:28:01 -05:00
ivy.xml	Updating the HybridSelectionPipeline for SnpEff 2.0.4 RC3	2011-11-17 14:46:12 -05:00