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R
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Now produces an expanded table at the start, as well
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2011-06-20 13:45:08 +00:00 |
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analysis/depristo
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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.
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2011-06-16 12:56:04 +00:00 |
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archive
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Removed unused importants, but some of these scripts are now out of date (they have been for a long time) so they don't compile anyway
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2011-05-22 18:43:48 +00:00 |
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c
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Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base.
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2010-12-17 14:49:15 +00:00 |
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chainFiles
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Renamed for consistency
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2011-05-25 02:12:21 +00:00 |
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doc
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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
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2010-08-19 00:42:37 +00:00 |
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java
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Reverting previous commit, as promised.
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2011-06-20 16:30:19 +00:00 |
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lua
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cleaned up the scripts and created an interval library to facilitate future reuse.
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2011-05-27 19:35:36 +00:00 |
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matlab
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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
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2009-11-30 20:02:25 +00:00 |
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packages
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Oops. Failed to add DbSnpMatchMetrics to Picard private jar.
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2011-06-14 15:14:19 +00:00 |
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perl
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Quit immediately with an error message if any of the individual steps fails.
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2011-04-22 13:23:33 +00:00 |
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python
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Rev Picard to get new PF_INDEL_RATE metric. Rev preQC generator script
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2011-06-14 17:43:43 +00:00 |
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ruby
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accidentally commited an old tool
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2010-08-25 15:42:02 +00:00 |
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scala
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Added stratification by discrete allele count, just like AF, but requiring genotypes so it can be exact. Added docs on wiki, and integrationtest using Kiran's very nice fundamental VCF
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2011-06-19 03:11:00 +00:00 |
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settings
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Rev Picard to get new PF_INDEL_RATE metric. Rev preQC generator script
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2011-06-14 17:43:43 +00:00 |
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shell
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Useful utility for looking at the file size of GSA file systems
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2011-04-02 03:47:27 +00:00 |
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testdata
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Updating VariantGaussianMixtureModelUnitTest to use truth sensitivity cutting
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2011-05-04 13:56:01 +00:00 |
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LICENSE
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Adding a license to the root directory in case BOSC checks for one. Has the
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2010-04-20 16:04:29 +00:00 |
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build.xml
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Fix for CoFoJa exception by upgrading to latest version
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2011-06-09 17:49:15 +00:00 |
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ivy.xml
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Factor out all testing dependencies into a separate test configuration and
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2011-05-05 22:42:11 +00:00 |
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