gatk-3.8

History

Ryan Poplin b57054c63c Various VQSR optimizations in both runtime and accuracy. -- For very large whole genome datasets with over 2M variants overlapping the training data randomly downsample the training set that gets used to build the Gaussian mixture model. -- Annotations are ordered by the difference in means between known and novel instead of by their standard deviation. -- Removed the training set quality score threshold. -- Now uses 2 gaussians by default for the negative model. -- Num bad argument has been removed and the cutoffs are now chosen by the model itself by looking at the LOD scores. -- Model plots are now generated much faster. -- Stricter threshold for determining model convergence. -- All VQSR integration tests change because of these changes to the model. -- Add test for downsampling of training data.	2013-11-29 13:04:46 -05:00
..
java	Various VQSR optimizations in both runtime and accuracy.	2013-11-29 13:04:46 -05:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00

Ryan Poplin b57054c63c Various VQSR optimizations in both runtime and accuracy.

-- For very large whole genome datasets with over 2M variants overlapping the training data randomly downsample the training set that gets used to build the Gaussian mixture model.
-- Annotations are ordered by the difference in means between known and novel instead of by their standard deviation.
-- Removed the training set quality score threshold.
-- Now uses 2 gaussians by default for the negative model.
-- Num bad argument has been removed and the cutoffs are now chosen by the model itself by looking at the LOD scores.
-- Model plots are now generated much faster.
-- Stricter threshold for determining model convergence.
-- All VQSR integration tests change because of these changes to the model.
-- Add test for downsampling of training data.

2013-11-29 13:04:46 -05:00

java

Various VQSR optimizations in both runtime and accuracy.

2013-11-29 13:04:46 -05:00

scala/test/org/broadinstitute/sting/queue/pipeline/examples

Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest

2013-02-27 04:45:53 -05:00