carneiro 28149e5c5e GenotypeAndValidate version 2, ready to be used. ... - now it differentiates between confident REF calls and not confident calls. - you can now use a BAM file as the truth set. - output is much clearer now dataProcessingPipeline version 2, ready to be used. - All the processing is now done at the sample level - Reads the input bam file headers to combine all lanes of the same sample. - Cleaning is now scattered/gathered. Inteligently breaks down in as many intervals as possible, given the dataset. - Outputs one processed bam file per sample (and a .list file with all processed files listed) - Much faster, low pass (read Papuans) can run in the hour queue. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5493 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-22 20:18:02 +00:00
..
carneiro	GenotypeAndValidate version 2, ready to be used.	2011-03-22 20:18:02 +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