kshakir f6d4b0aaf5 Using an embedded version of Picard for merging un-indexed bam files after scatter/gather instead of requiring the QScripts to specify the picard JAR. May do this for the GATK jar too. ... Fixed initialization of pending counts when using -startFromScratch so the count doesn't start at zero and end at -<#njobs>. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5483 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-21 18:20:01 +00:00
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carneiro	Using an embedded version of Picard for merging un-indexed bam files after scatter/gather instead of requiring the QScripts to specify the picard JAR. May do this for the GATK jar too.	2011-03-21 18:20:01 +00:00
chartl	Added in unit tests for the statistics calculated by the test runner; and bug-fixes to the calculations; so we have some assurance that the statistics coming out the back-end are correct.	2011-03-06 16:54:02 +00:00
delangel	Script for calling indels in all phase 1 samples - VQSR part still needs work but raw calling is done	2011-01-22 14:07:10 +00:00
depristo	BeagleOutputToVCF now accepts an option to keep monomorphic sites. This is useful to genotype a single sample, where having AC=0 just means that the sample is hom-ref at the site.	2011-03-18 03:08:38 +00:00
fromer	Some minor updates to fully utilize the functionality of reduceByInterval	2011-03-09 20:38:08 +00:00
hanna	Refactoring the qscript directory; oneoffs, playground, and core	2011-01-19 15:23:40 +00:00
kshakir	Removed deprecated getDbsnpFile.	2011-02-08 21:12:15 +00:00
rpoplin	not useful	2011-03-15 22:47:55 +00:00
QTools.q	Generalized association is now working. Output is in a horrific format. Implementation of T-testing. Improvements are to look for classes dynamically (a la VariantEval/VariantAnnotator), beautify output, and do optimizations where they exist.	2011-03-01 01:23:37 +00:00