zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk3的最后一个经典版本3.8
6,036 Commits
1 Branch
0 Tags
257 MiB
Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
Go to file
ebanks c2ec2891d1 Other people besides Mark also wanted VariantContext moved to the GATK, so I listened. I am moving VariantContext and all codecs that rely on it (VCF, SoapSNP, HapMap, and CGvar) to the GATK - including relevant unit tests and data files. Additionally, Matt has modified build.xml to generate the necessary jar files so that people can use our VCF codec with Tribble. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6077 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-06-24 16:56:04 +00:00
R Checkpointing some bugfixes with zero-length version directories and missing 2011-06-22 22:56:01 +00:00
analysis/depristo Simple program that calls indels in CEU trio exomes and WGS can compared the results. Overall the indel calls really look good to me, given reasonably good input BAM files. 2011-06-16 12:56:04 +00:00
archive Binomial and Multinomial interfaces for probability and coefficients in log and real space. Passed all unit tests. 2011-06-22 22:55:15 +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 Other people besides Mark also wanted VariantContext moved to the GATK, so I listened. I am moving VariantContext and all codecs that rely on it (VCF, SoapSNP, HapMap, and CGvar) to the GATK - including relevant unit tests and data files. Additionally, Matt has modified build.xml to generate the necessary jar files so that people can use our VCF codec with Tribble. 2011-06-24 16:56:04 +00:00
lua added comments on how to use this very useful script! 2011-06-22 22:55:50 +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 Checkpointing some bugfixes with zero-length version directories and missing 2011-06-22 22:56:01 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Other people besides Mark also wanted VariantContext moved to the GATK, so I listened. I am moving VariantContext and all codecs that rely on it (VCF, SoapSNP, HapMap, and CGvar) to the GATK - including relevant unit tests and data files. Additionally, Matt has modified build.xml to generate the necessary jar files so that people can use our VCF codec with Tribble. 2011-06-24 16:56:04 +00:00
settings Updated the tribble jar to revision 351 2011-06-22 22:55:57 +00:00
shell Useful utility for looking at the file size of GSA file systems 2011-04-02 03:47:27 +00:00
testdata Other people besides Mark also wanted VariantContext moved to the GATK, so I listened. I am moving VariantContext and all codecs that rely on it (VCF, SoapSNP, HapMap, and CGvar) to the GATK - including relevant unit tests and data files. Additionally, Matt has modified build.xml to generate the necessary jar files so that people can use our VCF codec with Tribble. 2011-06-24 16:56:04 +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 Other people besides Mark also wanted VariantContext moved to the GATK, so I listened. I am moving VariantContext and all codecs that rely on it (VCF, SoapSNP, HapMap, and CGvar) to the GATK - including relevant unit tests and data files. Additionally, Matt has modified build.xml to generate the necessary jar files so that people can use our VCF codec with Tribble. 2011-06-24 16:56:04 +00:00
ivy.xml A prototype script and library dependencies to extract a BAM list from a 2011-06-22 22:53:45 +00:00