gatk-3.8

gatk3的最后一个经典版本3.8

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depristo 38d7733989 Now accepts any number of VCFs to evaluate. Runs the standard (now three) variant eval commands and invokes the exomeQC R script. Has some annoying assumptions about paths encoded right now. Example usage below: setenv DATA ~/Desktop/broadLocal/localData/ java -Djava.io.tmpdir=tmp -jar ../dist/Queue.jar -S ../scala/qscript/oneoffs/depristo/ExomePostQCEval.scala --gatkjarfile ../dist/GenomeAnalysisTK.jar -R $DATA/human_g1k_v37.fasta $* -eval $DATA/ESPGO_Gabriel_NHLBI_eomi_june_2011_batch1.vcf -intervals ~/Desktop/broadLocal/localData/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list -dbSNP ~/Desktop/broadLocal/localData/dbsnp_132_b37.vcf -eval $DATA/ESPGO_Gabriel_NHLBI_eomi_june_2011_batch2.vcf git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6004 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-16 12:49:54 +00:00
R	Added density plots by sample for each metric. New command line argument ordering. No longer requires the per-sample.tsv suppl. data -- will conditionally load if available	2011-06-16 12:46:29 +00:00
analysis/depristo	CalibrateGenotypeLikelihoods now emits a molten data set with REF and ALT alleles, so that GL calibration can be evaluated as a function of the REF/ALT bases. DigestTable is a stand-alone Rscript that digests the multi-GB molten data table into a tiny table that shows reported vs. empirical GLs, as a function of a variety of features of the data, like REF/ALT, comp GT, eval GT, and GL itself.	2011-05-21 14:02:30 +00:00
archive	Removed unused importants, but some of these scripts are now out of date (they have been for a long time) so they don't compile anyway	2011-05-22 18:43:48 +00:00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
chainFiles	Renamed for consistency	2011-05-25 02:12:21 +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	Bringing VQSR up to date with the 1000G v2b changes	2011-06-14 20:23:43 +00:00
lua	cleaned up the scripts and created an interval library to facilitate future reuse.	2011-05-27 19:35:36 +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	Oops. Failed to add DbSnpMatchMetrics to Picard private jar.	2011-06-14 15:14:19 +00:00
perl	Quit immediately with an error message if any of the individual steps fails.	2011-04-22 13:23:33 +00:00
python	Rev Picard to get new PF_INDEL_RATE metric. Rev preQC generator script	2011-06-14 17:43:43 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Now accepts any number of VCFs to evaluate. Runs the standard (now three) variant eval commands and invokes the exomeQC R script. Has some annoying assumptions about paths encoded right now. Example usage below:	2011-06-16 12:49:54 +00:00
settings	Rev Picard to get new PF_INDEL_RATE metric. Rev preQC generator script	2011-06-14 17:43:43 +00:00
shell	Useful utility for looking at the file size of GSA file systems	2011-04-02 03:47:27 +00:00
testdata	Updating VariantGaussianMixtureModelUnitTest to use truth sensitivity cutting	2011-05-04 13:56:01 +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	Fix for CoFoJa exception by upgrading to latest version	2011-06-09 17:49:15 +00:00
ivy.xml	Factor out all testing dependencies into a separate test configuration and	2011-05-05 22:42:11 +00:00