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gatk3的最后一个经典版本3.8
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delangel a1653f0c83 Another major redo for indel genotyper: this time, add ability to do allele and variant discovery, and don't rely necessarily on external vcf's to provide candidate variants and alleles (e.g. by using IndelGenotyperV2). This has two major advantages: speed, and more fine-grained control of discovery process. Code is still under test and analysis but this version should be hopefully stable. 
Ability to genotype candidate variants from input vcf is retained and can be turned on by command line argument but is disabled by default. 
Code, by default, will build a consensus of the most common indel event at a pileup. If that consensus allele has a count bigger than N (=5 by default), we proceed to genotype by computing probabilistic realigmment, AF distribution etc. and possibly emmiting a call.

Needed for this, also added ability to build haplotypes from list of alleles instead of from a variant context.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4893 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-12-22 02:38:06 +00:00
R Vectorize() pDirectlyPhaseHetPairAtDistanceUsingDepth; deal with minor precision issues 2010-12-21 17:18:26 +00:00
archive Eric broke the build. Eric broke the build. 2010-12-15 17:01:38 +00:00
c Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base. 2010-12-17 14:49:15 +00:00
doc removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also 2010-08-19 00:42:37 +00:00
java Another major redo for indel genotyper: this time, add ability to do allele and variant discovery, and don't rely necessarily on external vcf's to provide candidate variants and alleles (e.g. by using IndelGenotyperV2). This has two major advantages: speed, and more fine-grained control of discovery process. Code is still under test and analysis but this version should be hopefully stable. 2010-12-22 02:38:06 +00:00
matlab Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function 2009-11-30 20:02:25 +00:00
packages Be certain to include core GATK reference metadata features and codecs in the 2010-12-21 21:30:07 +00:00
perl A helper script to merge two VCFs, run VariantEval, and the VariantReport.R script. 2010-11-28 00:45:21 +00:00
python Stabilitity improvements to GATK run report system. R code is now robust. XML parser uses the C backend in python, 10x faster. Added shell script that runs the daily reports, and linked the /humgen/ runme.csh to this script. Script now emails the group the daily PDFs to gsamembers 2010-12-15 14:56:12 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Committing my notes about the methods development pipeline so we stay synced up while I'm on vacation. Cheers. 2010-12-21 21:14:20 +00:00
settings Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
shell Stabilitity improvements to GATK run report system. R code is now robust. XML parser uses the C backend in python, 10x faster. Added shell script that runs the daily reports, and linked the /humgen/ runme.csh to this script. Script now emails the group the daily PDFs to gsamembers 2010-12-15 14:56:12 +00:00
testdata VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary 2010-11-15 22:19:22 +00:00
LICENSE Adding a license to the root directory in case BOSC checks for one. Has the 2010-04-20 16:04:29 +00:00
build.xml Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
ivy.xml Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00