gatk3的最后一个经典版本3.8

Mark DePristo 33b2f65bbd Script to evaluate SNP and indel calls for the experimental downsampler ... -- Calls NA12878 with and without the expt. downsampler on chr1 -- Creates combined vcf, annotating sites as overlapping omni SNPs and Mills indels -- Creates simple combined.table that has chr, pos, set, and type to easily ID missed good sites with the new downsampler		2012-09-26 11:33:06 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	RR bug: when determining the most common base at a position, break ties by which base has the highest sum of base qualities. Otherwise, sites with 1 Q2 N and 1 Q30 C are ending up as Ns in the consensus. I think perhaps we don't even care about which base has the most observations - it should just be determined by which has the highest sum of base qualities - but I'm not sure that's what users would expect.	2012-09-24 21:46:14 -04:00
public	Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable	2012-09-24 21:46:36 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00
.gitignore	a few more useful git ignores	2012-09-01 11:08:36 -04:00
build.xml	Proper error handling in NanoScheduler	2012-09-19 17:03:13 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00